# Job ID:6f062893-1e40-4e67-9d84-a65326867737 "# Metadata: variantvalidator_version: 2.2.1.dev691+g8946f76, variantvalidator_hgvs_version: 2.2.0, vvta_version: vvta_2024_01, vvseqrepo_db: VV_SR_2024_01/master, vvdb_version: vvdb_2024_5, options: transcript|genomic|protein|refseqgene|lrg|vcf|gene_info|tx_name|alt_loci" Input Warnings Select transcript HGVS_transcript HGVS_intronic_chr_context HGVS_intronic_rsg_context HGVS_RefSeqGene HGVS_LRG HGVS_LRG_transcript HGVS_Predicted_Protein HGVS_Genomic_GRCh37 HGVS_Genomic_GRCh38 GRCh37_CHR GRCh37_POS GRCh37_ID GRCh37_REF GRCh37_ALT GRCh38_CHR GRCh38_POS GRCh38_ID GRCh38_REF GRCh38_ALT Gene_Symbol HGNC_Gene_ID Transcript_description Alt_genomic_loci NM_001378609.3:c.351C>T MANE NM_001378609.3:c.351C>T NG_033008.2:g.127572C>T NP_001365538.2:p.(Asn117=) NC_000012.11:g.80615887C>T NC_000012.12:g.80222107C>T 12 80615887 . C T 12 80222107 . C T OTOGL HGNC:26901 "Homo sapiens otogelin like (OTOGL), transcript variant 3, mRNA" NM_001282684.2:c.405C>T MANE NM_001282684.2:c.405C>T NG_052003.1:g.10677C>T NP_001269613.2:p.(His135=) NC_000022.10:g.37453452C>T NC_000022.11:g.37057412C>T 22 37453452 . C T 22 37057412 . C T KCTD17 HGNC:25705 "Homo sapiens potassium channel tetramerization domain containing 17 (KCTD17), transcript variant 1, mRNA" NM_001378609.3:c.1981G>A MANE NM_001378609.3:c.1981G>A NG_033008.2:g.167525G>A NP_001365538.2:p.(Val661Met) NC_000012.11:g.80655840G>A NC_000012.12:g.80262060G>A 12 80655840 . G A 12 80262060 . G A OTOGL HGNC:26901 "Homo sapiens otogelin like (OTOGL), transcript variant 3, mRNA" NM_020884.7:c.4530G>C MANE NM_020884.7:c.4530G>C NG_016984.2:g.48495G>C NP_065935.4:p.(Lys1510Asn) NC_000020.10:g.33587198G>C NC_000020.11:g.34999395G>C 20 33587198 . G C 20 34999395 . G C MYH7B HGNC:15906 "Homo sapiens myosin heavy chain 7B (MYH7B), mRNA" NM_001006658.3:c.623_624del MANE NM_001006658.3:c.623_624del NP_001006659.1:p.(Pro208HisfsTer3) NC_000001.10:g.207642049_207642050del NC_000001.11:g.207468704_207468705del 1 207642043 . TCC T 1 207468698 . TCC T CR2 HGNC:2336 "Homo sapiens complement C3d receptor 2 (CR2), transcript variant 1, mRNA" NM_001382391.1:c.2259_2260del MANE NM_001382391.1:c.2259_2260del NG_034100.1:g.99097_99098del NP_001369320.1:p.(Glu755GlyfsTer30) NC_000008.10:g.68070699_68070700del NC_000008.11:g.67158464_67158465del 8 68070697 . CAA C 8 67158462 . CAA C CSPP1 HGNC:26193 "Homo sapiens centrosome and spindle pole associated protein 1 (CSPP1), transcript variant 8, mRNA" NM_006767.4:c.2348_2351del The current status of LRG_989 is pending therefore changes may be made to the LRG reference sequence MANE NM_006767.4:c.2348_2351del NG_034193.1:g.19640_19643del LRG_989:g.19640_19643del NP_006758.2:p.(Thr783ArgfsTer5) NC_000022.10:g.21351197_21351200del NC_000022.11:g.20996908_20996911del 22 21351195 . AACGC A 22 20996906 . AACGC A LZTR1 HGNC:6742 "Homo sapiens leucine zipper like post translational regulator 1 (LZTR1), mRNA" NM_000059.4:c.1053del MANE NM_000059.4:c.1053del NP_000050.3:p.(Lys351AsnfsTer16) NC_000013.10:g.32906668del NC_000013.11:g.32332531del 13 32906663 . GA G 13 32332526 . GA G BRCA2 HGNC:1101 "Homo sapiens BRCA2 DNA repair associated (BRCA2), transcript variant 1, mRNA" NM_000038.6:c.1908_1909dup MANE NM_000038.6:c.1908_1909dup NP_000029.2:p.(Gly637ValfsTer10) NC_000005.9:g.112170812_112170813dup NC_000005.10:g.112835115_112835116dup 5 112170810 . G GGT 5 112835113 . G GGT APC HGNC:583 "Homo sapiens APC regulator of WNT signaling pathway (APC), transcript variant 3, mRNA" NM_024577.4:c.819dup MANE NM_024577.4:c.819dup NP_078853.2:p.(Lys274Ter) NC_000005.9:g.148418040dup NC_000005.10:g.149038477dup 5 148418039 . T TA 5 149038476 . T TA SH3TC2 HGNC:29427 "Homo sapiens SH3 domain and tetratricopeptide repeats 2 (SH3TC2), mRNA" NM_001134673.4:c.243dup MANE NM_001134673.4:c.243dup NG_011787.2:g.16091dup NP_001128145.1:p.(Asp82ArgfsTer37) NC_000001.10:g.61554036dup NC_000001.11:g.61088364dup 1 61554033 . G GA 1 61088361 . G GA NFIA HGNC:7784 "Homo sapiens nuclear factor I A (NFIA), transcript variant 1, mRNA" NM_000277.3:c.667_674dup MANE NM_000277.3:c.667_674dup NG_008690.2:g.108236_108243dup NP_000268.1:p.(Gln226ThrfsTer118) NC_000012.11:g.103248946_103248953dup NC_000012.12:g.102855168_102855175dup 12 103248945 . G GGGAATGTT 12 102855167 . G GGGAATGTT PAH HGNC:8582 "Homo sapiens phenylalanine hydroxylase (PAH), transcript variant 1, mRNA" NM_000059.4:c.6449_6450insTA MANE NM_000059.4:c.6449_6450insTA NP_000050.3:p.(Lys2150AsnfsTer19) NC_000013.10:g.32914941_32914942insTA NC_000013.11:g.32340804_32340805insTA 13 32914940 . A AAT 13 32340803 . A AAT BRCA2 HGNC:1101 "Homo sapiens BRCA2 DNA repair associated (BRCA2), transcript variant 1, mRNA" NM_000642.3:c.36_37insCG MANE NM_000642.3:c.36_37insCG NG_012865.1:g.5995_5996insCG NP_000633.2:p.(Asn13ArgfsTer24) NC_000001.10:g.100316634_100316635insCG NC_000001.11:g.99851078_99851079insCG 1 100316633 . T TGC 1 99851077 . T TGC AGL HGNC:321 "Homo sapiens amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase (AGL), transcript variant 1, mRNA" NM_000532.5:c.433_434insGCTGTTA MANE NM_000532.5:c.433_434insGCTGTTA NG_008939.1:g.16631_16632insGCTGTTA NP_000523.2:p.(Met145SerfsTer18) NC_000003.11:g.135980797_135980798insGCTGTTA NC_000003.12:g.136261955_136261956insGCTGTTA 3 135980796 . C CAGCTGTT 3 136261954 . C CAGCTGTT PCCB HGNC:8654 "Homo sapiens propionyl-CoA carboxylase subunit beta (PCCB), transcript variant 1, mRNA; nuclear gene for mitochondrial product" NM_000112.4:c.1487_1488insGGCG MANE NM_000112.4:c.1487_1488insGGCG NP_000103.2:p.(Lys497AlafsTer2) NC_000005.9:g.149360643_149360644insGGCG NC_000005.10:g.149981080_149981081insGGCG 5 149360641 . T TCGGG 5 149981078 . T TCGGG SLC26A2 HGNC:10994 "Homo sapiens solute carrier family 26 member 2 (SLC26A2), mRNA" NM_015443.4:c.773_774inv MANE NM_015443.4:c.773_774inv NG_032784.1:g.59004_59005inv NP_056258.1:p.(Leu258Ser) NC_000017.10:g.44248736_44248737inv NC_000017.11:g.46171370_46171371inv 17 44248736 . CA TG 17 46171370 . CA TG KANSL1 HGNC:24565 "Homo sapiens KAT8 regulatory NSL complex subunit 1 (KANSL1), transcript variant 2, mRNA" NT_167251.1:g.617606_617607inv|NT_167251.2:g.615613_615614inv|NT_187663.1:g.873475_873476inv NM_000260.4:c.47_48inv The current status of LRG_1420 is pending therefore changes may be made to the LRG reference sequence MANE NM_000260.4:c.47_48inv NG_009086.2:g.19492_19493inv LRG_1420:g.19492_19493inv LRG_1420t1:c.47_48inv NP_000251.3:p.(Leu16Ser) NC_000011.9:g.76853783_76853784inv NC_000011.10:g.77142737_77142738inv 11 76853783 . TG CA 11 77142737 . TG CA MYO7A HGNC:7606 "Homo sapiens myosin VIIA (MYO7A), transcript variant 1, mRNA" NW_003871081.1:g.144373_144374inv NM_000545.8:c.1719_1720inv MANE NM_000545.8:c.1719_1720inv NP_000536.6:p.(Ser574Gly) NC_000012.11:g.121437381_121437382inv NC_000012.12:g.120999578_120999579inv 12 121437381 . CA TG 12 120999578 . CA TG HNF1A HGNC:11621 "Homo sapiens HNF1 homeobox A (HNF1A), transcript variant 2, mRNA" NM_000350.3:c.5843_5844inv MANE NM_000350.3:c.5843_5844inv NG_009073.2:g.117858_117859inv NP_000341.2:p.(Pro1948Leu) NC_000001.10:g.94473845_94473846inv NC_000001.11:g.94008289_94008290inv 1 94473845 . TG CA 1 94008289 . TG CA ABCA4 HGNC:34 "Homo sapiens ATP binding cassette subfamily A member 4 (ABCA4), transcript variant 1, mRNA" NM_000552.5:c.4222_4224del MANE NM_000552.5:c.4222_4224del NG_009072.2:g.110475_110477del NP_000543.3:p.(Lys1408del) NC_000012.11:g.6128370_6128372del NC_000012.12:g.6019204_6019206del 12 6128359 . CCTT C 12 6019193 . CCTT C VWF HGNC:12726 "Homo sapiens von Willebrand factor (VWF), mRNA" NC_000002.12:88452181:GGCGGGCGCGGCGGGCGCGG:GGCGGGCGCGGCGGGCGCGGCGGGCGCGG NC_000002.12:g.88452181GGCGGGCGCGGCGGGCGCGG>GGCGGGCGCGGCGGGCGCGGCGGGCGCGG automapped to NC_000002.12:g.88452200_88452201insCGGGCGCGG MANE NM_001135649.3:c.336_337insCGCGCCCGC NP_001129121.1:p.(Pro112_Ala113insArgAlaArg) NC_000002.11:g.88751719_88751720insCGGGCGCGG NC_000002.12:g.88452200_88452201insCGGGCGCGG 2 88751718 . C CGCGGGCGCG 2 88452199 . C CGCGGGCGCG FOXI3 HGNC:35123 "Homo sapiens forkhead box I3 (FOXI3), mRNA" NC_000007.14:g.131556290_131556295del MANE NM_001018111.3:c.84_89del NG_042104.1:g.5342_5347del NP_001018121.1:p.(Pro30_Ser31del) NC_000007.13:g.131241049_131241054del NC_000007.14:g.131556290_131556295del 7 131241029 . GGGCGAC G 7 131556270 . GGGCGAC G PODXL HGNC:9171 "Homo sapiens podocalyxin like (PODXL), transcript variant 1, mRNA" NC_000005.10:141945390:CTGCTGCTGCTGCTGCTGC:CTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC NC_000005.10:g.141945390CTGCTGCTGCTGCTGCTGC>CTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC automapped to NC_000005.10:g.141945408_141945409insTGCTGCTGCTGC MANE NM_016580.4:c.3527_3528insGCAGCAGCAGCA NP_057664.1:p.(Gly1176_Ser1177insGlnGlnGlnHis) NC_000005.9:g.141324973_141324974insTGCTGCTGCTGC NC_000005.10:g.141945408_141945409insTGCTGCTGCTGC 5 141324973 . G GTGCTGCTGCTGC 5 141945408 . G GTGCTGCTGCTGC PCDH12 HGNC:8657 "Homo sapiens protocadherin 12 (PCDH12), mRNA" NM_001378609.3:c.351C>T MANE NM_001378609.3:c.351C>T NG_033008.2:g.127572C>T NP_001365538.2:p.(Asn117=) NC_000012.11:g.80615887C>T NC_000012.12:g.80222107C>T 12 80615887 . C T 12 80222107 . C T OTOGL HGNC:26901 "Homo sapiens otogelin like (OTOGL), transcript variant 3, mRNA" NM_020884.7:c.2451G>A MANE NM_020884.7:c.2451G>A NG_016984.2:g.43252G>A NP_065935.4:p.(Ala817=) NC_000020.10:g.33581955G>A NC_000020.11:g.34994152G>A 20 33581955 . G A 20 34994152 . G A MYH7B HGNC:15906 "Homo sapiens myosin heavy chain 7B (MYH7B), mRNA" NM_001282684.2:c.405C>T MANE NM_001282684.2:c.405C>T NG_052003.1:g.10677C>T NP_001269613.2:p.(His135=) NC_000022.10:g.37453452C>T NC_000022.11:g.37057412C>T 22 37453452 . C T 22 37057412 . C T KCTD17 HGNC:25705 "Homo sapiens potassium channel tetramerization domain containing 17 (KCTD17), transcript variant 1, mRNA" NM_020884.7:c.1548C>T MANE NM_020884.7:c.1548C>T NG_016984.2:g.37323C>T NP_065935.4:p.(Phe516=) NC_000020.10:g.33576026C>T NC_000020.11:g.34988223C>T 20 33576026 . C T 20 34988223 . C T MYH7B HGNC:15906 "Homo sapiens myosin heavy chain 7B (MYH7B), mRNA" NM_001282684.2:c.55G>A MANE NM_001282684.2:c.55G>A NG_052003.1:g.5080G>A NP_001269613.2:p.(Ala19Thr) NC_000022.10:g.37447855G>A NC_000022.11:g.37051815G>A 22 37447855 . G A 22 37051815 . G A KCTD17 HGNC:25705 "Homo sapiens potassium channel tetramerization domain containing 17 (KCTD17), transcript variant 1, mRNA" NM_001101421.4:c.599G>T MANE NM_001101421.4:c.599G>T NP_001094891.4:p.(Ser200Ile) NC_000012.11:g.109838926G>T NC_000012.12:g.109401121G>T 12 109838926 . G T 12 109401121 . G T MYO1H HGNC:13879 "Homo sapiens myosin IH (MYO1H), mRNA" NM_001378609.3:c.1957T>G MANE NM_001378609.3:c.1957T>G NG_033008.2:g.167501T>G NP_001365538.2:p.(Cys653Gly) NC_000012.11:g.80655816T>G NC_000012.12:g.80262036T>G 12 80655816 . T G 12 80262036 . T G OTOGL HGNC:26901 "Homo sapiens otogelin like (OTOGL), transcript variant 3, mRNA" NM_001378609.3:c.1078C>T MANE NM_001378609.3:c.1078C>T NG_033008.2:g.157183C>T NP_001365538.2:p.(Arg360Ter) NC_000012.11:g.80645498C>T NC_000012.12:g.80251718C>T 12 80645498 . C T 12 80251718 . C T OTOGL HGNC:26901 "Homo sapiens otogelin like (OTOGL), transcript variant 3, mRNA" NM_001378609.3:c.1585C>T MANE NM_001378609.3:c.1585C>T NG_033008.2:g.160648C>T NP_001365538.2:p.(Gln529Ter) NC_000012.11:g.80648963C>T NC_000012.12:g.80255183C>T 12 80648963 . C T 12 80255183 . C T OTOGL HGNC:26901 "Homo sapiens otogelin like (OTOGL), transcript variant 3, mRNA" NM_014363.6:c.9219_9220del MANE NM_014363.6:c.9219_9220del NG_012342.1:g.104046_104047del NP_055178.3:p.(Cys3073Ter) NC_000013.10:g.23908797_23908798del NC_000013.11:g.23334658_23334659del 13 23908794 . TCA T 13 23334655 . TCA T SACS HGNC:10519 "Homo sapiens sacsin molecular chaperone (SACS), transcript variant 1, mRNA" NM_182961.4:c.482_483del MANE NM_182961.4:c.482_483del NG_012855.2:g.132108_132109del NP_892006.3:p.(Ser161Ter) NC_000006.11:g.152831428_152831429del NC_000006.12:g.152510293_152510294del 6 152831425 . CAG C 6 152510290 . CAG C SYNE1 HGNC:17089 "Homo sapiens spectrin repeat containing nuclear envelope protein 1 (SYNE1), transcript variant 1, mRNA" NM_005359.6:c.1245_1248del MANE NM_005359.6:c.1245_1248del NP_005350.1:p.(Asp415GlufsTer20) NC_000018.9:g.48593494_48593497del NC_000018.10:g.51067124_51067127del 18 48593490 . TAGAC T 18 51067120 . TAGAC T SMAD4 HGNC:6770 "Homo sapiens SMAD family member 4 (SMAD4), transcript variant 1, mRNA" NM_078480.3:c.382_383del MANE NM_078480.3:c.382_383del NG_033879.1:g.15886_15887del NP_510965.1:p.(Met128ValfsTer11) NC_000008.10:g.144900670_144900671del NC_000008.11:g.143818500_143818501del 8 144900669 . CAT C 8 143818499 . CAT C PUF60 HGNC:17042 "Homo sapiens poly(U) binding splicing factor 60 (PUF60), transcript variant 1, mRNA" NT_187571.1:g.295511_295512del|NW_003315923.1:g.157145_157146del NM_000059.3:c.4228_4229insA NM_000059.3:c.4228_4229insA automapped to NM_000059.3:c.4228dup|TranscriptVersionWarning: A more recent version of the selected reference sequence NM_000059.3 is available for genome build GRCh38 (NM_000059.4) RefSeq NM_000059.3:c.4228dup NG_012772.3:g.28104dup LRG_293:g.28104dup LRG_293t1:c.4228dup NP_000050.2:p.(Thr1410AsnfsTer4) NC_000013.10:g.32912720dup NC_000013.11:g.32338583dup 13 32912718 . T TA 13 32338581 . T TA BRCA2 HGNC:1101 "Homo sapiens BRCA2 DNA repair associated (BRCA2), mRNA" NM_001130987.1:c.3105dup TranscriptVersionWarning: A more recent version of the selected reference sequence NM_001130987.1 is available for genome build GRCh38 (NM_001130987.2) FALSE NM_001130987.1:c.3105dup LRG_845t2:c.3105dup NP_001124459.1:p.(Ile1036HisfsTer14) NC_000002.11:g.71797748dup NC_000002.12:g.71570618dup 2 71797746 . A AC 2 71570616 . A AC DYSF HGNC:3097 "Homo sapiens dysferlin (DYSF), transcript variant 1, mRNA" NM_000277.3:c.1355dup MANE NM_000277.3:c.1355dup NG_008690.2:g.124232dup NP_000268.1:p.(Ter453ValextTer35) NC_000012.11:g.103232959dup NC_000012.12:g.102839181dup 12 103232956 . C CT 12 102839178 . C CT PAH HGNC:8582 "Homo sapiens phenylalanine hydroxylase (PAH), transcript variant 1, mRNA" NM_000155.4:c.1138T>C MANE NM_000155.4:c.1138T>C NG_009029.2:g.8859T>C NP_000146.2:p.(Ter380ArgextTer49) NC_000009.11:g.34650444T>C NC_000009.12:g.34650447T>C 9 34650444 . T C 9 34650447 . T C GALT HGNC:4135 "Homo sapiens galactose-1-phosphate uridylyltransferase (GALT), transcript variant 1, mRNA" NM_001110792.2:c.1497A>G MANE NM_001110792.2:c.1497A>G NG_007107.3:g.111737A>G NP_001104262.1:p.(Ter499TrpextTer27) NC_000023.10:g.153295818T>C NC_000023.11:g.154030367T>C X 153295818 . T C X 154030367 . T C MECP2 HGNC:6990 "Homo sapiens methyl-CpG binding protein 2 (MECP2), transcript variant 2, mRNA" NW_003871103.3:g.1464346T>C NM_145038.5:c.2223A>C MANE NM_145038.5:c.2223A>C NG_042824.1:g.59606A>C NP_659475.2:p.(Ter741CysextTer13) NC_000002.11:g.26679385A>C NC_000002.12:g.26456517A>C 2 26679385 . A C 2 26456517 . A C DRC1 HGNC:24245 "Homo sapiens dynein regulatory complex subunit 1 (DRC1), mRNA" NM_000033.4:c.234_242del MANE NM_000033.4:c.234_242del NG_009022.2:g.5633_5641del NP_000024.2:p.(Arg80_Leu82del) NC_000023.10:g.152990955_152990963del NC_000023.11:g.153725500_153725508del X 152990950 . TGGCTCCTGC T X 153725495 . TGGCTCCTGC T ABCD1 HGNC:61 "Homo sapiens ATP binding cassette subfamily D member 1 (ABCD1), mRNA" NW_003871103.3:g.1159483_1159491del NM_001145026.2:c.147_158del MANE NM_001145026.2:c.147_158del NG_034052.1:g.5488_5499del NP_001138498.1:p.(Thr51_Thr54del) NC_000012.11:g.80838613_80838624del NC_000012.12:g.80444833_80444844del 12 80838610 . AGTGACAACAAAT A 12 80444830 . AGTGACAACAAAT A PTPRQ HGNC:9679 "Homo sapiens protein tyrosine phosphatase receptor type Q (PTPRQ), mRNA" NM_000102.4:c.334_336dup MANE NM_000102.4:c.334_336dup NG_007955.1:g.7178_7180dup NP_000093.1:p.(Ile112dup) NC_000010.10:g.104595111_104595113dup NC_000010.11:g.102835354_102835356dup 10 104595110 . C CGAT 10 102835353 . C CGAT CYP17A1 HGNC:2593 "Homo sapiens cytochrome P450 family 17 subfamily A member 1 (CYP17A1), mRNA" NM_000156.6:c.507_521dup MANE NM_000156.6:c.507_521dup NG_009785.1:g.7575_7589dup NP_000147.1:p.(Cys169_Ser173dup) NC_000019.9:g.1398967_1398981dup NC_000019.10:g.1398968_1398982dup 19 1398963 . C CCAGGAGGTGAGGTTG 19 1398964 . C CCAGGAGGTGAGGTTG GAMT HGNC:4136 "Homo sapiens guanidinoacetate N-methyltransferase (GAMT), transcript variant 1, mRNA"