Variant Detail

Variant Information
ID
DPV: 1742
Chromosome
10
Gene
HGVS (GRCh37/hg19)
NC_000010.10:g.73545397G>A
HGVS (GRCh38/hg38)
NC_000010.11:g.71785640G>A
HGVS (RNA)
NM_022124.5:c.5722G>A
HGVS (Protein)
NP_071407.4:p.V1908I
dbSNP
-
ClinGen Allele Registry
CA245698
Allele Frequency
Individual Information

ID
DPVS:1590.1
Clinical Significance
Pathogenic
Date Last Evaluated
2018-01-30
Clinical Significance Citation
Sakuma, N. An effective screening strategy for deafness in combination with a next-generation sequencing platform: a consecutive analysis. 2016 J Hum Genet. 2016 Mar;61(3):253-61. doi: 10.1038/jhg.2015.143. Epub 2016 Jan 14. PMID:26763877

Transcript
-
Disease

Phenotype
-
Zygosity
single heterozygote
Allele Origin
germline
Affected Status
yes
Sample Type
  • DNA
Analysis Type
  • Next-Generation Sequencing
Collection Method
literature only
Compound heterozygous variant(s)
Data Submitter
Comment
-

ID
DPVS:1833.1
Clinical Significance
Uncertain significance
Date Last Evaluated
2018-03-30
Clinical Significance Citation
Mizutari, K. High prevalence of CDH23 mutations in patients with congenital high-frequency sporadic or recessively inherited hearing loss. 2015 Orphanet J Rare Dis. 2015 May 13;10:60. doi: 10.1186/s13023-015-0276-z. PMID:25963016

Transcript
-
Disease

Phenotype
-
Zygosity
single heterozygote
Allele Origin
germline
Affected Status
yes
Sample Type
  • DNA
Analysis Type
  • SEQuencing
Collection Method
literature only
Compound heterozygous variant(s)
Data Submitter
Comment
-

ID
DPVS:1999.1
Clinical Significance
Pathogenic
Date Last Evaluated
2018-05-30
Clinical Significance Citation
-
Transcript
-
Disease

Phenotype
-
Zygosity
compound heterozygote
Allele Origin
germline
Affected Status
yes
Sample Type
  • DNA
Analysis Type
  • SEQuencing
Collection Method
clinical testing
Compound heterozygous variant(s)
Data Submitter
Comment
This variant was detected in  IRUD (Initiative on Rare and Undiagnosed Diseases) project.

ClinVar
Model Animals
VCF
VCF (GRCh37/hg19)
											##fileformat=VCFv4.0
##reference=GRCh37
##INFO=<ID=CLNALLELEID,Number=1,Type=Integer,Description="the ClinVar Allele ID">
##INFO=<ID=CLNDISDB,Number=.,Type=String,Description="Tag-value pairs of disease database name and identifier, e.g. OMIM:NNNNNN (from ClinVar)">
##INFO=<ID=CLNDN,Number=.,Type=String,Description="ClinVar's preferred disease name for the concept specified by disease identifiers in CLNDISDB (from ClinVar)">
##INFO=<ID=CLNHGVS,Number=.,Type=String,Description="Top-level (primary assembly, alt, or patch) HGVS expression.(from ClinVar)">
##INFO=<ID=CLNSIG,Number=.,Type=String,Description="Clinical significance for this single variant (from ClinVar)">
##INFO=<ID=EXAC_AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed (from ExAC r1)">
##INFO=<ID=EXAC_AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed (from ExAC r1)">
##INFO=<ID=EXAC_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from ExAC r1)">
##INFO=<ID=EXAC_FILTER,Number=1,Type=String,Description="calculated by self of overlapping values in field FILTER (from ExAC r1)">
##INFO=<ID=GNOMAD_AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed (from gnomAD v2.1.1 )">
##INFO=<ID=GNOMAD_AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed (from gnomAD v2.1.1 )">
##INFO=<ID=GNOMAD_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from gnomAD v2.1.1 )">
##INFO=<ID=HGVD_AAF,Number=A,Type=Float,Description="Alternative Allele Frequency(s) NA/(NR+NAtotal) (from HGVD/DBexome20170802)">
##INFO=<ID=HGVD_AC,Number=A,Type=Integer,Description="number(s) of alternative allele(s) (from HGVD/DBexome20170802)">
##INFO=<ID=HGVD_NR,Number=1,Type=Integer,Description="number of reference allele (from HGVD/DBexome20170802)">
##INFO=<ID=TOMMO_4_7K_AC,Number=A,Type=Integer,Description="Allele count in genotypes (from ToMMo 4.7KJPN (20190826))">
##INFO=<ID=TOMMO_4_7K_AF,Number=A,Type=Float,Description="Allele frequency, for each ALT allele, in the same order as listed  (from ToMMo 4.7KJPN (20190826))">
##INFO=<ID=TOMMO_4_7K_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from ToMMo 4.7KJPN (20190826))">
##INFO=<ID=dbSNP_RSID,Number=1,Type=String,Description="dbSNP ID (from dbSNP b151 )">
##INFO=<ID=GENEINFO,Number=1,Type=String,Description="Pairs each of gene symbol:gene id. The gene symbol and id are delimited by a colon (:)">
##INFO=<ID=DPVID,Number=.,Type=String,Description="DPV Variant ID">
##INFO=<ID=DPVSIG,Number=.,Type=String,Description="Variant Clinical Significance">
##INFO=<ID=DPVDSDBID,Number=.,Type=String,Description="Variant disease database ID">
##INFO=<ID=DPVDBN,Number=.,Type=String,Description="Variant disease name">
##INFO=<ID=DPVHGVS,Number=.,Type=String,Description="Variant in HGVS.">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
10	73545397	NC_000010.10:g.73545397G>A	G	A	.	.	EXAC_AF=0.0003802;EXAC_AC=46;EXAC_AN=120974;GNOMAD_AF=0.00041587;GNOMAD_AC=94;GNOMAD_AN=226030;TOMMO_4_7K_AF=0.0036;TOMMO_4_7K_AC=34;TOMMO_4_7K_AN=9546;CLNALLELEID=194667;CLNDN=Usher_syndrome_type_1|Usher_syndrome_type_1D|Deafness,_autosomal_recessive_12|not_specified|not_provided;CLNDISDB=MONDO:MONDO:0010168,MedGen:C1568247,OMIM:276900,Orphanet:ORPHA231169|MONDO:MONDO:0010984,MedGen:C1832845,OMIM:601067|MONDO:MONDO:0011067,MedGen:C1832394,OMIM:601386|MedGen:CN169374|MedGen:CN517202;CLNSIG=Conflicting_interpretations_of_pathogenicity;CLNHGVS=NC_000010.10:g.73545397G>A;HGVD_AAF=0.003722;HGVD_NR=2409;HGVD_AC=9;GENEINFO=13733:64072;DPVID=1742;DPVSIG=Pathogenic|Uncertain_significance;DPVDSDBID=OMIM:601067|OMIM:601386;DPVDBN=Usher_syndrome_1D/F|Deafness\x2c_autosomal_recessive\x2c_12;DPVHGVS=NC_000010.10:g.73545397G>A	.
										
VCF (GRCh38/hg38)
											##fileformat=VCFv4.0
##reference=GRCh38
##INFO=<ID=CLNALLELEID,Number=1,Type=Integer,Description="the ClinVar Allele ID">
##INFO=<ID=CLNDISDB,Number=.,Type=String,Description="Tag-value pairs of disease database name and identifier, e.g. OMIM:NNNNNN (from ClinVar)">
##INFO=<ID=CLNDN,Number=.,Type=String,Description="ClinVar's preferred disease name for the concept specified by disease identifiers in CLNDISDB (from ClinVar)">
##INFO=<ID=CLNHGVS,Number=.,Type=String,Description="Top-level (primary assembly, alt, or patch) HGVS expression.(from ClinVar)">
##INFO=<ID=CLNSIG,Number=.,Type=String,Description="Clinical significance for this single variant (from ClinVar)">
##INFO=<ID=GNOMAD_AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed (from gnomAD v2.1.1 )">
##INFO=<ID=GNOMAD_AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed (from gnomAD v2.1.1 )">
##INFO=<ID=GNOMAD_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from gnomAD v2.1.1 )">
##INFO=<ID=dbSNP_RSID,Number=1,Type=String,Description="dbSNP ID (from dbSNP b151 )">
##originalFile=</tmp/crossmap-input-okjglhrz>
##targetRefGenome=</usr/lib64/python2.7/site-packages/transvar/transvar.download/hg38.fa>
##INFO=<ID=GENEINFO,Number=1,Type=String,Description="Pairs each of gene symbol:gene id. The gene symbol and id are delimited by a colon (:)">
##INFO=<ID=DPVID,Number=.,Type=String,Description="DPV Variant ID">
##INFO=<ID=DPVSIG,Number=.,Type=String,Description="Variant Clinical Significance">
##INFO=<ID=DPVDSDBID,Number=.,Type=String,Description="Variant disease database ID">
##INFO=<ID=DPVDBN,Number=.,Type=String,Description="Variant disease name">
##INFO=<ID=DPVHGVS,Number=.,Type=String,Description="Variant in HGVS.">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
10	71785640	NC_000010.10:g.73545397G>A	G	A	.	.	dbSNP_RSID=rs368828743;GNOMAD_AF=0.00041587;GNOMAD_AC=94;GNOMAD_AN=226030;CLNALLELEID=194667;CLNDN=Usher_syndrome_type_1|Usher_syndrome_type_1D|Deafness,_autosomal_recessive_12|not_specified|not_provided;CLNDISDB=MONDO:MONDO:0010168,MedGen:C1568247,OMIM:276900,Orphanet:ORPHA231169|MONDO:MONDO:0010984,MedGen:C1832845,OMIM:601067|MONDO:MONDO:0011067,MedGen:C1832394,OMIM:601386|MedGen:CN169374|MedGen:CN517202;CLNSIG=Conflicting_interpretations_of_pathogenicity;CLNHGVS=NC_000010.11:g.71785640G>A;GENEINFO=13733:64072;DPVID=1742;DPVSIG=Pathogenic|Uncertain_significance;DPVDSDBID=OMIM:601067|OMIM:601386;DPVDBN=Usher_syndrome_1D/F|Deafness\x2c_autosomal_recessive\x2c_12;DPVHGVS=NC_000010.11:g.71785640G>A	.