diff --git a/tests/benchmark_hgvs.py b/tests/benchmark_hgvs.py new file mode 100755 index 0000000..fb44286 --- /dev/null +++ b/tests/benchmark_hgvs.py @@ -0,0 +1,133 @@ +#!/bin/env python3 +import time +from argparse import ArgumentParser + +import hgvs +import hgvs.dataproviders.uta +from hgvs.assemblymapper import AssemblyMapper +from hgvs.exceptions import HGVSDataNotAvailableError, HGVSInvalidVariantError + +from cdot.hgvs.dataproviders import JSONDataProvider, RESTDataProvider + + +def handle_args(): + parser = ArgumentParser(description='Benchmark cdot') + parser.add_argument("hgvs_file") + group = parser.add_mutually_exclusive_group() + group.add_argument('--uta', action='store_true') + group.add_argument('--rest', action='store_true') + parser.add_argument('--json', help='JSON file') + args = parser.parse_args() + if not any([args.uta, args.rest, args.json]): + parser.error("You need to specify at least one of 'uta', 'rest', 'json'") + return args + + +def main(): + args = handle_args() + + hgvs_g_c_list = [] + with open(args.hgvs_file) as f: + for line in f: + hgvs_g_c_list.append(line.split()) + + total = len(hgvs_g_c_list) + print(f"Using {total} test records") + + if args.uta: + hdp = hgvs.dataproviders.uta.connect() + elif args.rest: + hdp = RESTDataProvider() # Uses API server at cdot.cc + elif args.json: + hdp = JSONDataProvider({"GRCh38": args.json}) + + am = AssemblyMapper(hdp, + assembly_name='GRCh38', + alt_aln_method='splign', replace_reference=True) + + hp = hgvs.parser.Parser() + + run_times = [] + correct = 0 + incorrect = 0 + no_data = 0 + for hgvs_g, hgvs_c in hgvs_g_c_list: + start = time.time() + try: + var_c = hp.parse_hgvs_variant(hgvs_c) + if ":c." in hgvs_c: + converted_hgvs_g = str(am.c_to_g(var_c)) + else: + converted_hgvs_g = str(am.n_to_g(var_c)) + except HGVSDataNotAvailableError: + no_data += 1 + continue + except HGVSInvalidVariantError as ive: + print(f"{hgvs_c}: {ive}") + incorrect += 1 + continue + + if converted_hgvs_g == hgvs_g: + correct += 1 + else: + incorrect += 1 + print(f"{hgvs_c}: '{hgvs_g}' != '{converted_hgvs_g}' (actual)") + continue + + end = time.time() + time_taken = end - start + run_times.append(time_taken) + + print(f"Total: {total}, correct: {correct}, incorrect: {incorrect}, no data: {no_data}") + print(run_times) + + +if __name__ == '__main__': + main() + +""" + +* Get a subset of rows from ClinVar VCF + * zgrep "^#" clinvar.vcf.gz > header.txt + * zcat -v "^#" clinvar.vcf.gz | shuf -n 1000 > clinvar_1k_records.vcf + * cat header.txt clinvar_1k_rows.vcf | gzip > clinvar_1k.vcf.gz + +* Annotate the VCF to get MANE transcript (via --pick) + + vep -i clinvar_1k.vcf.gz -o clinvar_1k.vep_annotated.vcf.gz --cache --dir /data/annotation/VEP/vep_cache --fasta /data/annotation/fasta/GCF_000001405.39_GRCh38.p13_genomic.fna.gz --assembly GRCh38 --offline --use_given_ref --vcf --compress_output gzip --force_overwrite --pick --no_escape --hgvs --refseq --buffer_size 1000 + +* Extract out the g.HGVS and c.HGVS + + + + +def cyvcf2_header_types(cyvcf2_reader): + header_types = defaultdict(dict) + for h in cyvcf2_reader.header_iter(): + info = h.info() + h_id = info.get("ID") + if h_id: # Not much use w/o this + header_types[h.type][h_id] = info + return header_types + + +reader = Reader("./clinvar_1k.vcf.gz") +header_types = cyvcf2_header_types(reader) +description = header_types["INFO"]["CSQ"]["description"] +description = description.replace('"', '') # Strip double quotes + +match = "Format: " +columns_str = description[description.rfind(match) + len(match):] +vep_columns = columns_str.split("|") + +hgvs = [] +for v in reader: + csq = v.INFO.get("CSQ") + td = dict(zip(vep_columns, csq.split("|"))) + g_hgvs = v.INFO.get("CLNHGVS") + c_hgvs = td.get("HGVSc") + if g_hgvs and c_hgvs: + hgvs.append((g_hgvs, c_hgvs)) + + +""" \ No newline at end of file diff --git a/tests/test_data/clinvar_hgvs_010.tsv b/tests/test_data/clinvar_hgvs_010.tsv new file mode 100644 index 0000000..22b2a20 --- /dev/null +++ b/tests/test_data/clinvar_hgvs_010.tsv @@ -0,0 +1,10 @@ +NC_000002.12:g.189003410G>A NM_000090.4:c.2554-1G>A +NC_000002.12:g.73572910G>A NM_015120.4:c.11036G>A +NC_000003.12:g.36996633_36996634delinsTT NM_001354619.1:c.-593_-592delinsTT +NC_000003.12:g.58149866C>T NM_001164317.2:c.6201C>T +NC_000006.12:g.52082460T>C NM_138694.4:c.213A>G +NC_000007.14:g.98906228C>T NM_001244580.1:c.1088C>T +NC_000010.11:g.120905027T>C NM_018117.12:c.3193+216T>C +NC_000012.12:g.8854218G>A NM_144670.6:c.2681G>A +NC_000016.10:g.81869317C>T NM_002661.5:c.564+19C>T +NC_000017.11:g.58734198A>G NM_058216.3:c.1107A>G diff --git a/tests/test_data/clinvar_hgvs_050.tsv b/tests/test_data/clinvar_hgvs_050.tsv new file mode 100644 index 0000000..63c05d5 --- /dev/null +++ b/tests/test_data/clinvar_hgvs_050.tsv @@ -0,0 +1,50 @@ +NC_000001.11:g.237617406G>A NM_001035.3:c.5836G>A +NC_000001.11:g.33021456_33021458del NM_001625.4:c.336_338del +NC_000001.11:g.52383874T>C NM_004153.4:c.1819A>G +NC_000001.11:g.52397773C>T NM_004153.4:c.314G>A +NC_000001.11:g.53213501A>C NM_000098.3:c.1883A>C +NC_000001.11:g.94047046C>T NM_000350.3:c.2791G>A +NC_000002.12:g.169275142G>A NM_004525.3:c.1869C>T +NC_000002.12:g.178538451C>G NM_001267550.2:c.99289+89G>C +NC_000002.12:g.178608202G>T NM_001267550.2:c.52681C>A +NC_000002.12:g.178741896G>A NM_001267550.2:c.11337C>T +NC_000002.12:g.214781051A>T NM_000465.4:c.823T>A +NC_000002.12:g.219490515_219490517del NM_005876.5:c.9028_9030del +NC_000002.12:g.46909034C>T NM_001171511.2:c.93-1065G>A +NC_000002.12:g.47806494A>C NM_001281493.1:c.2938A>C +NC_000002.12:g.47813341T>C NM_001190274.2:c.2120A>G +NC_000002.12:g.85888897C>A NM_003896.4:c.9G>T +NC_000003.12:g.123752448G>C NM_001321309.2:c.-155-12447C>G +NC_000005.10:g.10255709T>C NM_012073.5:c.332-246T>C +NC_000005.10:g.112841537T>A NM_000038.6:c.5943T>A +NC_000005.10:g.139026767A>G NM_022464.5:c.645+34T>C +NC_000005.10:g.149027638G>A NM_024577.4:c.2094C>T +NC_000005.10:g.35873480C>T NM_002185.5:c.538C>T +NC_000007.14:g.16089456T>C NM_001101426.4:c.*2239A>G +NC_000007.14:g.97852358C>T NM_001673.5:c.1587G>A +NC_000008.11:g.18062326C>A NM_177924.5:c.601G>T +NC_000008.11:g.89980722C>T NM_002485.5:c.480+12G>A +NC_000009.12:g.37784879T>G NM_016042.4:c.166A>C +NC_000009.12:g.69035905C>T NM_000144.5:c.123C>T +NC_000010.11:g.87925523T>C NM_000314.8:c.175T>C +NC_000011.10:g.112045279del NR_164072.1:n.1167+49del +NC_000011.10:g.118312837C>T NM_000733.4:c.323C>T +NC_000011.10:g.17427125C>T NR_147094.2:n.2212G>A +NC_000011.10:g.64809875del NM_130804.2:c.237del +NC_000012.12:g.120737861C>T NM_000017.4:c.497C>T +NC_000013.11:g.27920121C>T NM_000209.4:c.-18C>T +NC_000014.9:g.30879438C>T NM_004086.3:c.389C>T +NC_000016.10:g.89770196G>A NM_000135.4:c.2286C>T +NC_000017.11:g.43045725C>T NR_027676.2:n.5722G>A +NC_000017.11:g.43094198del NR_027676.2:n.1510del +NC_000017.11:g.59031925C>T NM_015294.6:c.1919G>A +NC_000017.11:g.80058782T>C NM_017950.4:c.1318-76T>C +NC_000018.10:g.58343058C>G NM_001144967.3:c.1530C>G +NC_000018.10:g.70176380_70176383del NM_173630.4:c.1476+295_1476+298del +NC_000019.10:g.12897438G>A NM_000159.4:c.1082+10G>A +NC_000021.9:g.42477365G>A NM_080860.4:c.653C>T +NC_000022.11:g.17110140A>G NM_001289905.1:c.*320A>G +NC_000023.11:g.154767342C>T NM_001363.5:c.600C>T +NC_000023.11:g.19355691T>C NM_000284.4:c.765T>C +NC_000023.11:g.45059450G>A NR_111960.1:n.1555G>A +NC_000023.11:g.74742052G>A NM_001008537.3:c.2505C>T diff --git a/tests/test_data/clinvar_hgvs_100.tsv b/tests/test_data/clinvar_hgvs_100.tsv new file mode 100644 index 0000000..846a310 --- /dev/null +++ b/tests/test_data/clinvar_hgvs_100.tsv @@ -0,0 +1,100 @@ +NC_000001.11:g.12007126G>A NM_001127660.1:c.1946G>A +NC_000001.11:g.21860220G>A NM_005529.7:c.4971C>T +NC_000001.11:g.237643408G>C NM_001035.3:c.7303G>C +NC_000001.11:g.23808165T>C NM_000191.3:c.720A>G +NC_000001.11:g.241517292C>A NM_000143.4:c.157G>T +NC_000001.11:g.94111501G>A NM_000350.3:c.239C>T +NC_000002.12:g.113220093C>T NM_003466.4:c.1275G>A +NC_000002.12:g.144399194T>C NM_014795.4:c.1993A>G +NC_000002.12:g.15286830T>C NM_015909.4:c.5138+243A>G +NC_000002.12:g.178592272G>A NM_001267550.2:c.59632C>T +NC_000002.12:g.178715710C>T NM_001267550.2:c.25704G>A +NC_000002.12:g.214745103C>G NM_000465.4:c.1867G>C +NC_000002.12:g.47803493G>C NM_001281493.1:c.2340G>C +NC_000002.12:g.73432303A>G NM_015120.4:c.1432+12A>G +NC_000002.12:g.73453022T>C NM_015120.4:c.6498T>C +NC_000002.12:g.85343265G>T NM_017750.4:c.1810C>A +NC_000002.12:g.85888897C>A NM_003896.4:c.9G>T +NC_000003.12:g.15644611A>G NM_001281723.3:c.695A>G +NC_000003.12:g.158691443T>C NR_164500.1:n.2195T>C +NC_000003.12:g.43598588T>A NM_018075.5:c.416A>T +NC_000003.12:g.49099390C>T NM_005051.3:c.1568G>A +NC_000003.12:g.49099430C>T NM_005051.3:c.1528G>A +NC_000003.12:g.52402867A>G NM_004656.4:c.1895T>C +NC_000003.12:g.69118837G>T NM_001304418.3:c.1518C>A +NC_000004.12:g.112646986A>G NM_016648.4:c.552+31A>G +NC_000004.12:g.113355165A>G NM_001148.6:c.6547A>G +NC_000004.12:g.43030609T>A NM_001080476.2:c.*69T>A +NC_000004.12:g.52038248C>A NM_000232.5:c.12G>T +NC_000004.12:g.83273598C>T NM_015697.8:c.590G>A +NC_000004.12:g.88268819C>T NM_152542.5:c.629G>A +NC_000005.10:g.113064054C>G NM_001085377.2:c.2143G>C +NC_000005.10:g.126550263C>A NM_001182.5:c.1348G>T +NC_000005.10:g.179126029C>T NM_014244.5:c.2719G>A +NC_000005.10:g.79051354T>C NM_013391.3:c.678A>G +NC_000005.10:g.83539495C>T NM_004385.5:c.6492C>T +NC_000006.12:g.129280072C>T NM_001079823.2:c.2462C>T +NC_000006.12:g.129353296C>A NM_001079823.2:c.4656C>A +NC_000006.12:g.52079909A>G NM_138694.4:c.381T>C +NC_000006.12:g.52082460T>C NM_138694.4:c.213A>G +NC_000007.14:g.22945636C>G NM_032581.4:c.1519G>C +NC_000007.14:g.5999116G>C NM_000535.7:c.697C>G +NC_000007.14:g.93146872C>A NM_152703.5:c.-779+11G>T +NC_000008.11:g.89980722C>T NM_002485.5:c.480+12G>A +NC_000009.12:g.2717979G>A NM_133497.4:c.240G>A +NC_000009.12:g.34648800G>A NM_001258332.1:c.399G>A +NC_000009.12:g.37745681G>A NM_014907.3:c.3649G>A +NC_000009.12:g.69035905C>T NM_000144.5:c.123C>T +NC_000009.12:g.92045993A>G NM_006415.4:c.1136+6T>C +NC_000010.11:g.110784352G>A NM_001134363.3:c.1349G>A +NC_000010.11:g.110799819A>G NM_001134363.3:c.1701A>G +NC_000010.11:g.111013593T>C NR_136749.1:n.2936T>C +NC_000011.10:g.112045279del NR_164072.1:n.1167+49del +NC_000011.10:g.118503818del NM_001197104.2:c.7926del +NC_000011.10:g.119026031A>G NM_001164279.2:c.701T>C +NC_000011.10:g.1752849G>A NM_001909.5:c.*654C>T +NC_000011.10:g.47342611del NM_000256.3:c.1595del +NC_000011.10:g.5226575del NM_000518.5:c.315+2del +NC_000011.10:g.61445957A>G NM_017841.4:c.387A>G +NC_000013.11:g.32332371_32332377delinsTACTTCAG NM_000059.3:c.893_899delinsTACTTCAG +NC_000013.11:g.32337627T>C NM_000059.3:c.3272T>C +NC_000013.11:g.32339462G>C NM_000059.3:c.5107G>C +NC_000014.9:g.23432514G>C NM_000257.4:c.503-8C>G +NC_000014.9:g.45176022C>G NM_020937.4:c.3268C>G +NC_000014.9:g.67766373A>G NM_015346.4:c.5865T>C +NC_000014.9:g.89980550C>G NM_018319.4:c.802C>G +NC_000014.9:g.92006041T>C NM_004239.4:c.1935A>G +NC_000015.10:g.90754814G>A NM_000057.4:c.963G>A +NC_000015.10:g.92985680G>T NM_001271.4:c.3413+7G>T +NC_000016.10:g.1352026C>T NM_032520.5:c.52+9C>T +NC_000016.10:g.173193A>G NM_000517.6:c.164A>G +NC_000016.10:g.2046301C>G NM_002528.7:c.181G>C +NC_000016.10:g.2048728T>C NM_000548.5:c.113T>C +NC_000016.10:g.2081776T>C NM_000548.5:c.3792T>C +NC_000016.10:g.2109256C>T NM_000296.4:c.5911G>A +NC_000016.10:g.30993204G>T NM_052874.5:c.712C>A +NC_000017.11:g.41769530G>A NM_002230.4:c.356C>T +NC_000017.11:g.43094198del NR_027676.2:n.1510del +NC_000017.11:g.50356597T>C NM_022167.4:c.1569T>C +NC_000017.11:g.59031925C>T NM_015294.6:c.1919G>A +NC_000017.11:g.65557863T>A NM_004655.4:c.758A>T +NC_000017.11:g.65557982_65557984del NM_004655.4:c.639_641del +NC_000018.10:g.46639718G>A NM_144612.6:c.409C>T +NC_000018.10:g.70176380_70176383del NM_173630.4:c.1476+295_1476+298del +NC_000019.10:g.13298566C>T NM_001127222.2:c.3067G>A +NC_000019.10:g.48969229T>A NM_002103.5:c.*59A>T +NC_000019.10:g.51353233dup NM_001014763.1:c.551dup +NC_000019.10:g.53904356T>C NM_002739.5:c.1657-279T>C +NC_000019.10:g.54191771C>T NM_001077446.4:c.294C>T +NC_000019.10:g.54193391G>A NM_001077446.4:c.*29G>A +NC_000020.11:g.10658702_10658703insA NM_000214.3:c.459_460insT +NC_000020.11:g.10673008T>C NM_000214.3:c.82-2A>G +NC_000020.11:g.31831073G>A NM_033118.4:c.1356G>A +NC_000020.11:g.35504820_35504831del NM_007186.6:c.6451_6462del +NC_000020.11:g.63494913G>A NM_001958.5:c.513C>T +NC_000021.9:g.32678630del NM_003895.3:c.1627+15del +NC_000021.9:g.34370822G>T NM_172201.1:c.344G>T +NC_000021.9:g.45468322G>A NM_130445.4:c.187G>A +NC_000021.9:g.45511078A>C NM_130445.4:c.3694-33A>C +NC_000023.11:g.22221720T>C NM_000444.6:c.1876T>C +NC_000023.11:g.41343808_41343809dup NR_126093.1:n.1696_1697dup diff --git a/tests/test_data/clinvar_hgvs_500.tsv b/tests/test_data/clinvar_hgvs_500.tsv new file mode 100644 index 0000000..5deafab --- /dev/null +++ b/tests/test_data/clinvar_hgvs_500.tsv @@ -0,0 +1,500 @@ +NC_000001.11:g.10271557G>A NM_001365951.3:c.776G>A +NC_000001.11:g.10475012G>A NM_004565.3:c.36+10G>A +NC_000001.11:g.107777269A>G NM_006113.5:c.408T>C +NC_000001.11:g.115696823C>G NM_138959.3:c.*5444C>G +NC_000001.11:g.12007126G>A NM_001127660.1:c.1946G>A +NC_000001.11:g.1214053G>A NM_003327.4:c.75C>T +NC_000001.11:g.154167941C>T NM_152263.4:c.855-1G>A +NC_000001.11:g.156138758G>A NM_170707.4:c.1968+1G>A +NC_000001.11:g.160231339T>C NR_028104.2:n.1487A>G +NC_000001.11:g.16991953G>A NM_022089.4:c.2126+56C>T +NC_000001.11:g.197421267G>A NM_201253.3:c.1439G>A +NC_000001.11:g.197477654A>G NM_201253.3:c.4006-10A>G +NC_000001.11:g.201066922C>A NM_000069.3:c.2622G>T +NC_000001.11:g.201078052C>T NM_000069.3:c.1446G>A +NC_000001.11:g.202596820G>A NM_177402.5:c.1197C>T +NC_000001.11:g.209785625C>T NM_006147.4:c.*2795G>A +NC_000001.11:g.21228061_21228062delinsCC NM_001397.3:c.1671-21_1671-20delinsGG +NC_000001.11:g.214644678A>G NM_016343.4:c.5108A>G +NC_000001.11:g.216418655A>G NM_206933.3:c.510T>C +NC_000001.11:g.21860220G>A NM_005529.7:c.4971C>T +NC_000001.11:g.225839929A>G NM_001136018.3:c.823A>G +NC_000001.11:g.236739394C>T NM_001278344.1:c.345C>T +NC_000001.11:g.236751504C>T NM_001278344.1:c.1067C>T +NC_000001.11:g.237591290A>G NM_001035.3:c.4160+298A>G +NC_000001.11:g.237617406G>A NM_001035.3:c.5836G>A +NC_000001.11:g.237625796A>G NM_001035.3:c.6158A>G +NC_000001.11:g.237643408G>C NM_001035.3:c.7303G>C +NC_000001.11:g.23808151G>A NM_000191.3:c.734C>T +NC_000001.11:g.23808165T>C NM_000191.3:c.720A>G +NC_000001.11:g.241517292C>A NM_000143.4:c.157G>T +NC_000001.11:g.29230712C>T NM_016011.5:c.176+19G>A +NC_000001.11:g.33021456_33021458del NM_001625.4:c.336_338del +NC_000001.11:g.39283113A>G NM_012090.5:c.711-76A>G +NC_000001.11:g.43433189C>T NM_001365999.1:c.5803C>T +NC_000001.11:g.45334400C>T NR_146882.1:n.364G>A +NC_000001.11:g.46192545C>T NM_001243766.1:c.1257G>A +NC_000001.11:g.52383874T>C NM_004153.4:c.1819A>G +NC_000001.11:g.52397773C>T NM_004153.4:c.314G>A +NC_000001.11:g.53213501A>C NM_000098.3:c.1883A>C +NC_000001.11:g.54758839T>C NM_152268.4:c.323A>G +NC_000001.11:g.62496461G>C NM_001367561.1:c.4801C>G +NC_000001.11:g.7738307C>T NM_015215.4:c.4007C>T +NC_000001.11:g.77929344C>G NM_144573.3:c.893C>G +NC_000001.11:g.94021716T>C NM_000350.3:c.4774-2A>G +NC_000001.11:g.94111501G>A NM_000350.3:c.239C>T +NC_000001.11:g.99884619A>T NM_000642.3:c.2597A>T +NC_000001.11:g.99916693T>G NM_000642.3:c.4443T>G +NC_000002.12:g.108758454A>G NM_006267.5:c.2508A>G +NC_000002.12:g.15286830T>C NM_015909.4:c.5138+243A>G +NC_000002.12:g.162318171A>G NM_022168.4:c.137T>C +NC_000002.12:g.165949651C>T NM_024753.5:c.95G>A +NC_000002.12:g.165991601G>A NR_148667.2:n.6091C>T +NC_000002.12:g.166242651C>T NR_110260.1:n.612-5544C>T +NC_000002.12:g.169275142G>A NM_004525.3:c.1869C>T +NC_000002.12:g.172488237G>C NM_001079818.3:c.2505+9G>C +NC_000002.12:g.174944936C>T NR_038133.2:n.223G>A +NC_000002.12:g.178544424G>T NM_001267550.2:c.95805C>A +NC_000002.12:g.178552825C>T NM_001267550.2:c.90075G>A +NC_000002.12:g.178568869G>A NM_001267550.2:c.77263C>T +NC_000002.12:g.178573111A>C NM_001267550.2:c.73021T>G +NC_000002.12:g.178580169A>T NM_001267550.2:c.67118T>A +NC_000002.12:g.178635556A>T NM_001267550.2:c.41768T>A +NC_000002.12:g.178649809A>G NM_001267550.2:c.39895+8T>C +NC_000002.12:g.178715025C>T NM_001267550.2:c.26161G>A +NC_000002.12:g.178715710C>T NM_001267550.2:c.25704G>A +NC_000002.12:g.178739946A>G NM_001267550.2:c.13287T>C +NC_000002.12:g.178741896G>A NM_001267550.2:c.11337C>T +NC_000002.12:g.189003410G>A NM_000090.4:c.2554-1G>A +NC_000002.12:g.189006207G>A NM_000090.4:c.3041G>A +NC_000002.12:g.189041608C>T NM_000393.5:c.3611G>A +NC_000002.12:g.201160763G>A NM_003879.7:c.1125G>A +NC_000002.12:g.201628118G>A NM_001044385.3:c.901C>T +NC_000002.12:g.202377495del NM_001204.7:c.21del +NC_000002.12:g.21002185del NM_000384.3:c.13238del +NC_000002.12:g.214728771G>A NM_000465.4:c.2239C>T +NC_000002.12:g.214745103C>G NM_000465.4:c.1867G>C +NC_000002.12:g.214780584A>T NM_000465.4:c.1290T>A +NC_000002.12:g.214780754C>T NM_000465.4:c.1120G>A +NC_000002.12:g.214781051A>T NM_000465.4:c.823T>A +NC_000002.12:g.215404492C>G NM_001306132.1:c.3150G>C +NC_000002.12:g.219490515_219490517del NM_005876.5:c.9028_9030del +NC_000002.12:g.219500146T>C NM_001374295.1:c.66T>C +NC_000002.12:g.223777862A>C NM_001039569.2:c.11T>G +NC_000002.12:g.232770984G>A NM_002242.4:c.379C>T +NC_000002.12:g.240025261G>C NM_004544.4:c.41C>G +NC_000002.12:g.241734690T>G NM_152783.5:c.-98T>G +NC_000002.12:g.241850169C>T NM_005018.3:c.*889G>A +NC_000002.12:g.25235677C>T NR_135490.2:n.3027+30G>A +NC_000002.12:g.27459470C>T NM_015662.3:c.2695G>A +NC_000002.12:g.29070735T>C NM_001029883.3:c.3527A>G +NC_000002.12:g.39022807A>G NM_005633.3:c.1621T>C +NC_000002.12:g.39120392A>G NM_005633.3:c.31T>C +NC_000002.12:g.43973845G>T NM_133259.4:c.1211C>A +NC_000002.12:g.43995716C>T NM_133259.4:c.149+83G>A +NC_000002.12:g.44320515G>C NM_000341.4:c.1934G>C +NC_000002.12:g.47806494A>C NM_001281493.1:c.2938A>C +NC_000002.12:g.47813341T>C NM_001190274.2:c.2120A>G +NC_000002.12:g.50053295G>A NM_001330078.2:c.4104C>T +NC_000002.12:g.50922680C>T NM_001330078.2:c.798G>A +NC_000002.12:g.69327047T>C NM_002056.4:c.1868A>G +NC_000002.12:g.71600774C>T NM_001130987.2:c.3829C>T +NC_000002.12:g.73432303A>G NM_015120.4:c.1432+12A>G +NC_000002.12:g.73572910G>A NM_015120.4:c.11036G>A +NC_000002.12:g.84441031T>C NM_003849.4:c.589+16A>G +NC_000002.12:g.85663814G>A NM_000542.5:c.706C>T +NC_000002.12:g.88627005C>G NM_004836.7:c.270G>C +NC_000002.12:g.96265375del NM_001193304.3:c.7del +NC_000002.12:g.96711664T>A NM_001322351.1:c.341A>T +NC_000003.12:g.122911499T>C NM_001031702.4:c.3083A>G +NC_000003.12:g.123752448G>C NM_001321309.2:c.-155-12447C>G +NC_000003.12:g.128481943G>A 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+NC_000003.12:g.51984133C>G NM_001316331.2:c.339C>G +NC_000003.12:g.52408496T>C NM_004656.4:c.233A>G +NC_000003.12:g.53660158T>C NM_001128840.3:c.649T>C +NC_000003.12:g.58136073T>A NM_001164317.2:c.4859T>A +NC_000003.12:g.69118837G>T NM_001304418.3:c.1518C>A +NC_000003.12:g.8990718T>C NM_014850.4:c.2680A>G +NC_000004.12:g.112646007_112646008dup NM_016648.4:c.203-344_203-343dup +NC_000004.12:g.113288192C>T NM_001148.6:c.2179-196C>T +NC_000004.12:g.113353759A>G NM_001148.6:c.5141A>G +NC_000004.12:g.113355165A>G NM_001148.6:c.6547A>G +NC_000004.12:g.123314015G>A NM_145207.3:c.2633G>A +NC_000004.12:g.128959622T>G NM_144643.4:c.1025A>C +NC_000004.12:g.150908712G>A NM_001367550.1:c.1307C>T +NC_000004.12:g.169424634C>T NR_164630.1:n.3603G>A +NC_000004.12:g.182654203C>T NM_001080477.4:c.1111+310C>T +NC_000004.12:g.186287735A>G NR_033900.1:n.1066+693T>C +NC_000004.12:g.186595616G>A NM_005245.4:c.13138+73C>T +NC_000004.12:g.2830139G>A NM_001122681.2:c.1233G>A +NC_000004.12:g.39205260A>G NM_025132.4:c.710A>G +NC_000004.12:g.43030609T>A NM_001080476.2:c.*69T>A +NC_000004.12:g.52038248C>A NM_000232.5:c.12G>T +NC_000004.12:g.54270644A>C NM_006206.6:c.1133A>C +NC_000004.12:g.54289022G>T NM_006206.6:c.2788G>T +NC_000004.12:g.6302153C>T NM_006005.3:c.2358C>T +NC_000004.12:g.83273598C>T NM_015697.8:c.590G>A +NC_000004.12:g.87614948_87614965del NM_014208.3:c.2286_2303del +NC_000004.12:g.95154894C>T NM_001203.3:c.*221C>T +NC_000004.12:g.99608764A>G NM_000253.3:c.1558-2A>G +NC_000005.10:g.110746452T>C NM_138773.4:c.462+106T>C +NC_000005.10:g.112707552C>T NM_001354897.2:c.-166C>T +NC_000005.10:g.112801339C>G NM_000038.6:c.790C>G +NC_000005.10:g.112814272C>T NM_000038.6:c.835-1223C>T +NC_000005.10:g.112819225A>G NM_000038.6:c.1193A>G +NC_000005.10:g.112840059T>C NM_000038.6:c.4465T>C +NC_000005.10:g.112840795A>G NM_000038.6:c.5201A>G +NC_000005.10:g.112841537T>A NM_000038.6:c.5943T>A +NC_000005.10:g.112842303C>T NM_000038.6:c.6709C>T +NC_000005.10:g.113064054C>G NM_001085377.2:c.2143G>C +NC_000005.10:g.126543129G>T NM_001182.5:c.*1836C>A +NC_000005.10:g.126550263C>A NM_001182.5:c.1348G>T +NC_000005.10:g.128537568G>A NM_001999.4:c.36C>T +NC_000005.10:g.138575298A>C NM_004134.7:c.21T>G +NC_000005.10:g.138886249C>A NM_001903.5:c.1100C>A +NC_000005.10:g.138924511G>C NM_001903.5:c.1548G>C +NC_000005.10:g.138933987G>T NM_001903.5:c.2619G>T +NC_000005.10:g.139026767A>G NM_022464.5:c.645+34T>C +NC_000005.10:g.14716776G>T NM_054027.6:c.1071C>A +NC_000005.10:g.149027638G>A NM_024577.4:c.2094C>T +NC_000005.10:g.159323269C>T NM_002187.3:c.149G>A +NC_000005.10:g.170027937C>G NR_156756.1:n.3559C>G +NC_000005.10:g.178990692G>A NM_000843.4:c.912C>T +NC_000005.10:g.179126029C>T NM_014244.5:c.2719G>A +NC_000005.10:g.180631842T>C NM_182925.5:c.59-64A>G +NC_000005.10:g.223510G>A NM_004168.4:c.92G>A +NC_000005.10:g.225496C>T NM_004168.4:c.390C>T +NC_000005.10:g.35873480C>T NM_002185.5:c.538C>T +NC_000005.10:g.36241699_36241700delinsAT NM_001085411.3:c.99_100delinsAT +NC_000005.10:g.36976674G>A NM_133433.4:c.1495+272G>A +NC_000005.10:g.37815660_37815665del NM_000514.4:c.625_630del +NC_000005.10:g.53101492A>C NM_004531.5:c.244T>G +NC_000005.10:g.78816382G>A NM_000046.5:c.1213+22974C>T +NC_000005.10:g.7896138G>A NM_002454.3:c.1676+286G>A +NC_000005.10:g.79051354T>C NM_013391.3:c.678A>G +NC_000005.10:g.83539495C>T NM_004385.5:c.6492C>T +NC_000005.10:g.90684082G>A NM_032119.4:c.6161G>A +NC_000005.10:g.90690351C>G NM_032119.4:c.6706+275C>G +NC_000005.10:g.90848705T>C NM_032119.4:c.17088T>C +NC_000006.12:g.129280072C>T NM_001079823.2:c.2462C>T +NC_000006.12:g.135411365T>C NM_001134831.2:c.2944A>G +NC_000006.12:g.137871530T>C NM_001270508.2:c.295+8T>C +NC_000006.12:g.151436126dup NM_017909.4:c.613+333dup +NC_000006.12:g.16327384A>C NM_000332.3:c.927T>G +NC_000006.12:g.24503390_24503391insTTGCCCT NM_001080.3:c.566_567insTTGCCCT +NC_000006.12:g.29673379A>G NM_001366333.2:c.516T>C +NC_000006.12:g.38842808G>A NM_001206927.2:c.4750G>A +NC_000006.12:g.44301248G>A NM_020745.4:c.2701C>T +NC_000006.12:g.49607202del NM_000324.3:c.1086del +NC_000006.12:g.51649178C>A NM_138694.4:c.11217G>T +NC_000006.12:g.51911883T>C NM_138694.4:c.6406A>G +NC_000006.12:g.51912568G>A NM_138694.4:c.6130C>T +NC_000006.12:g.52022809G>T NM_138694.4:c.5372C>A +NC_000006.12:g.52027863A>G NM_138694.4:c.3594T>C +NC_000006.12:g.52082460T>C NM_138694.4:c.213A>G +NC_000006.12:g.52490335C>T NM_018100.4:c.1836C>T +NC_000006.12:g.73479839A>G NM_133645.3:c.933A>G +NC_000006.12:g.7568073C>T NM_004415.4:c.1266+167C>T +NC_000006.12:g.7582959C>T NM_004415.4:c.5697C>T +NC_000006.12:g.99613768_99613769insGCCGCT NM_021620.4:c.1133_1134insGCCGCT +NC_000007.14:g.117536672C>T NM_000492.4:c.868C>T +NC_000007.14:g.117590352G>A NM_000492.4:c.1680-1G>A +NC_000007.14:g.117590405C>T NM_000492.4:c.1732C>T +NC_000007.14:g.117611690T>A NM_000492.4:c.3249T>A +NC_000007.14:g.124858948_124858949delinsCA NM_015450.3:c.702+8_702+9delinsTG +NC_000007.14:g.128838784C>T NM_001127487.2:c.1392C>T +NC_000007.14:g.150950013G>T NM_000238.4:c.2398+155C>A +NC_000007.14:g.150974951C>G NM_000238.4:c.77-10G>C +NC_000007.14:g.151675582C>T NM_016203.4:c.522G>A +NC_000007.14:g.152676043C>G NM_005431.2:c.37G>C +NC_000007.14:g.21681356C>T NM_001277115.2:c.5329-190C>T +NC_000007.14:g.21892699T>C NM_001277115.2:c.12750+32T>C +NC_000007.14:g.22945636C>G NM_032581.4:c.1519G>C +NC_000007.14:g.5987206del NM_000535.7:c.1559del +NC_000007.14:g.5989799C>A NM_000535.7:c.1144+1G>T +NC_000007.14:g.92001185A>T NM_147185.3:c.1268A>T +NC_000007.14:g.92001314G>A NM_147185.3:c.1397G>A +NC_000007.14:g.92083295A>C NM_147185.3:c.8262A>C +NC_000007.14:g.92225826T>C NM_001350672.1:c.1148A>G +NC_000007.14:g.93146872C>A NM_152703.5:c.-779+11G>T +NC_000007.14:g.93477671G>A NM_001742.4:c.206-3C>T +NC_000007.14:g.98962620C>T NM_001244580.1:c.6808+193C>T +NC_000008.11:g.132908271G>A NM_003235.5:c.3933G>A +NC_000008.11:g.133238787C>T NM_001258432.2:c.*91G>A +NC_000008.11:g.18062326C>A NM_177924.5:c.601G>T +NC_000008.11:g.19951805G>C NM_000237.3:c.286G>C +NC_000008.11:g.41692693C>T NM_001142446.2:c.3936G>A +NC_000008.11:g.47939665C>T NM_001081640.2:c.999G>A +NC_000008.11:g.60862233C>T NM_017780.4:c.7868C>T +NC_000008.11:g.70596318T>C NM_014294.6:c.430A>G +NC_000008.11:g.89970536C>T NM_002485.5:c.724G>A +NC_000008.11:g.89971253T>G NM_002485.5:c.622A>C +NC_000008.11:g.99817804G>A NM_017890.4:c.8436+1G>A +NC_000009.12:g.105774107A>C NM_018112.3:c.*27A>C +NC_000009.12:g.114167972C>T NM_032888.4:c.417C>T +NC_000009.12:g.127682541A>G NM_001374309.2:c.1641A>G +NC_000009.12:g.130458605A>G NM_054012.4:c.363+16A>G +NC_000009.12:g.131066964G>A NM_006059.4:c.2352G>A +NC_000009.12:g.133439362C>T NR_024514.2:n.993-4C>T +NC_000009.12:g.133454548C>T NR_024514.2:n.2013C>T +NC_000009.12:g.135768940G>A NM_020822.3:c.1510+3G>A +NC_000009.12:g.135786208G>C NM_020822.3:c.3189G>C +NC_000009.12:g.136519192C>T NM_017617.5:c.865+251G>A +NC_000009.12:g.137716838_137716839delinsAT NM_024757.5:c.298_299delinsAT +NC_000009.12:g.2717979G>A NM_133497.4:c.240G>A +NC_000009.12:g.27220096C>T NM_000459.4:c.3151C>T +NC_000009.12:g.37745681G>A NM_014907.3:c.3649G>A +NC_000009.12:g.37784879T>G NM_016042.4:c.166A>C +NC_000009.12:g.92031834C>G NM_006415.4:c.*631G>C +NC_000009.12:g.94603360G>A NM_001127628.2:c.*21C>T +NC_000009.12:g.99138008T>C NM_004612.4:c.724T>C +NC_000010.11:g.102399333A>G NM_001322934.2:c.1163A>G +NC_000010.11:g.102837127G>C NM_000102.4:c.235C>G +NC_000010.11:g.113583298G>C NM_004132.5:c.1177G>C +NC_000010.11:g.120905027T>C NM_018117.12:c.3193+216T>C +NC_000010.11:g.124405517T>C NM_001171814.1:c.153A>G +NC_000010.11:g.14926890C>G NM_001033855.3:c.925G>C +NC_000010.11:g.16824378T>G NM_001081.4:c.*597A>C +NC_000010.11:g.43119586C>T NM_020975.6:c.2448C>T +NC_000010.11:g.49619800T>A NM_020984.3:c.109T>A +NC_000010.11:g.67219752G>A NM_013266.4:c.698C>T +NC_000010.11:g.71704709C>T NM_022124.6:c.2734-202C>T +NC_000010.11:g.84202978A>T NM_033100.4:c.640-2A>T +NC_000010.11:g.84252930T>C NM_001012720.2:c.432T>C +NC_000010.11:g.86687079C>T NM_001368064.1:c.690-4817C>T +NC_000010.11:g.87933267A>G NM_000314.8:c.492+16A>G +NC_000010.11:g.94304582T>G NM_016341.4:c.5559T>G +NC_000011.10:g.101491986G>A NM_004621.6:c.946-248C>T +NC_000011.10:g.108317472T>C NM_000051.3:c.6298T>C +NC_000011.10:g.108365387T>C NM_000051.3:c.9050T>C +NC_000011.10:g.118312837C>T NM_000733.4:c.323C>T +NC_000011.10:g.118501694A>G NM_001197104.2:c.6342A>G +NC_000011.10:g.118503818del NM_001197104.2:c.7926del +NC_000011.10:g.118504239A>G NM_001197104.2:c.8347A>G +NC_000011.10:g.119026031A>G NM_001164279.2:c.701T>C +NC_000011.10:g.119029299T>C NM_001164279.2:c.-172+93A>G +NC_000011.10:g.119100852G>A NM_001382.4:c.283-9C>T +NC_000011.10:g.121125573T>C NM_005422.2:c.1475T>C +NC_000011.10:g.1752849G>A NM_001909.5:c.*654C>T +NC_000011.10:g.17552090C>T NM_001277269.2:c.328+15C>T +NC_000011.10:g.47332243dup NM_000256.3:c.3644dup +NC_000011.10:g.47337494C>T NM_000256.3:c.2499G>A +NC_000011.10:g.47342611del NM_000256.3:c.1595del +NC_000011.10:g.61950564G>A NM_004183.4:c.-37+137G>A +NC_000011.10:g.64804618_64804619del NM_130804.2:c.1563_1564del +NC_000011.10:g.66851130G>A NM_001040716.2:c.2133C>T +NC_000011.10:g.68773349T>C NM_001876.4:c.1656A>G +NC_000011.10:g.71435394A>T NM_001163817.2:c.1409T>A +NC_000011.10:g.72234279A>C NM_001567.4:c.2213-2A>C +NC_000011.10:g.78732326G>A NM_001098816.3:c.3128C>T +NC_000012.12:g.101764513G>A NM_024312.5:c.2404C>T +NC_000012.12:g.108536790C>T NM_014706.4:c.1310-5G>A +NC_000012.12:g.119701660C>T NM_001206999.2:c.5506G>A +NC_000012.12:g.120737861C>T NM_000017.4:c.497C>T +NC_000012.12:g.123621806C>T NM_001414.4:c.868G>A +NC_000012.12:g.20679921_20679922insC NM_000921.4:c.3185-109_3185-108insC +NC_000012.12:g.32792669G>A NM_004572.3:c.2552C>T +NC_000012.12:g.32792719G>C NM_004572.3:c.2502C>G +NC_000012.12:g.42460293T>A NM_153026.3:c.2012A>T +NC_000012.12:g.51774224C>T 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+NC_000013.11:g.48459955_48459982del NM_000321.2:c.2106+122_2106+149del +NC_000014.9:g.101980063T>C NM_001376.5:c.774+89T>C +NC_000014.9:g.102431959C>T NM_014844.5:c.1248C>T +NC_000014.9:g.23415684A>T NM_000257.4:c.5102T>A +NC_000014.9:g.23432514G>C NM_000257.4:c.503-8C>G +NC_000014.9:g.24160500C>T NM_017999.5:c.3166-20C>T +NC_000014.9:g.30880264C>A NM_004086.3:c.437-188C>A +NC_000014.9:g.50145431T>C NM_006939.4:c.2504+46A>G +NC_000014.9:g.67766373A>G NM_015346.4:c.5865T>C +NC_000014.9:g.77616609C>G NM_004863.3:c.-30G>C +NC_000014.9:g.89980550C>G NM_018319.4:c.802C>G +NC_000014.9:g.92006041T>C NM_004239.4:c.1935A>G +NC_000015.10:g.100152774G>A NM_139057.4:c.1323-12C>T +NC_000015.10:g.25339189_25339190del NR_148916.2:n.3079_3080del +NC_000015.10:g.25360443C>T NR_148916.2:n.2205G>A +NC_000015.10:g.27870944G>A NM_000275.3:c.2244+210C>T +NC_000015.10:g.42384500C>T NM_000070.3:c.327C>T +NC_000015.10:g.45105691C>T NM_001363711.2:c.2286G>A +NC_000015.10:g.48421540G>A NM_000138.5:c.7699+18C>T +NC_000015.10:g.48508701A>G NM_000138.5:c.1718T>C +NC_000015.10:g.48520724T>A NM_000138.5:c.1082A>T +NC_000015.10:g.48526169G>A NM_000138.5:c.949C>T +NC_000015.10:g.48613076A>G NM_000138.5:c.181T>C +NC_000015.10:g.50925230T>G NM_007347.5:c.542+11T>G +NC_000015.10:g.55437099_55440647del NM_130810.4:c.784-1037_894-2012del +NC_000015.10:g.66435151G>A NM_002755.4:c.205G>A +NC_000015.10:g.89776621G>A NM_001039958.2:c.264G>A +NC_000015.10:g.89777047A>G NM_001039958.2:c.690A>G +NC_000015.10:g.89805203G>T NM_001150.3:c.772C>A +NC_000015.10:g.90754814G>A NM_000057.4:c.963G>A +NC_000015.10:g.90763153G>A NM_000057.4:c.2070G>A +NC_000015.10:g.92939571A>G NM_001271.4:c.552-7A>G +NC_000015.10:g.92985680G>T NM_001271.4:c.3413+7G>T +NC_000015.10:g.98963177T>C NM_000875.5:c.*5735T>C +NC_000016.10:g.1210090G>A NM_021098.3:c.3800G>A +NC_000016.10:g.1352026C>T NM_032520.5:c.52+9C>T +NC_000016.10:g.15717248C>G NM_002474.3:c.5396G>C +NC_000016.10:g.15798685G>A NM_002474.3:c.505C>T +NC_000016.10:g.173193A>G 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