Variant Detail

Variant Information
ID
DPV: 9905
Chromosome
9
Gene
HGVS (GRCh37/hg19)
NC_000009.11:g.36236825T>C
HGVS (GRCh38/hg38)
NC_000009.12:g.36236828T>C
HGVS (RNA)
NM_001128227.2:c.862+4A>G
HGVS (Protein)
dbSNP
-
ClinGen Allele Registry
CA10627319
Allele Frequency
Individual Information

ID
DPVS:10715.2
Clinical Significance
Pathogenic
Date Last Evaluated
2019-03-29
Clinical Significance Citation
Nishino, I. Distal myopathy with rimmed vacuoles is allelic to hereditary inclusion body myopathy. 2002 Neurology. 2002 Dec 10;59(11):1689-93. doi: 10.1212/01.wnl.0000041631.28557.c6. PMID:12473753

Transcript
-
Disease

Phenotype
-
Zygosity
compound heterozygote
Allele Origin
unknown
Affected Status
yes
Sample Type
  • DNA
Analysis Type
  • SEQuencing
Collection Method
clinical testing
Compound heterozygous variant(s)
Data Submitter
Comment
c.[620A>T];[862+4A>G]|c.[862+4A>G];[1807G>C]

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
9	36236825	NC_000009.11:g.36236825T>C	T	C	.	.	CLNALLELEID=308336;CLNDN=Sialuria|GNE_myopathy;CLNDISDB=MONDO:MONDO:0010028,MedGen:C0342853,OMIM:269921,Orphanet:ORPHA3166,SNOMED_CT:238051008|MONDO:MONDO:0011603,MedGen:C1853926,OMIM:605820,Orphanet:ORPHA602;CLNSIG=Uncertain_significance;CLNHGVS=NC_000009.11:g.36236825T>C;GENEINFO=23657:10020;DPVID=9905;DPVSIG=Pathogenic;DPVDSDBID=OMIM:605820;DPVDBN=Nonaka_myopathy;DPVHGVS=NC_000009.11:g.36236825T>C	.
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-zndiybml>
##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
9	36236828	NC_000009.11:g.36236825T>C	T	C	.	.	dbSNP_RSID=rs886063926;CLNALLELEID=308336;CLNDN=Sialuria|GNE_myopathy;CLNDISDB=MONDO:MONDO:0010028,MedGen:C0342853,OMIM:269921,Orphanet:ORPHA3166,SNOMED_CT:238051008|MONDO:MONDO:0011603,MedGen:C1853926,OMIM:605820,Orphanet:ORPHA602;CLNSIG=Uncertain_significance;CLNHGVS=NC_000009.12:g.36236828T>C;GENEINFO=23657:10020;DPVID=9905;DPVSIG=Pathogenic;DPVDSDBID=OMIM:605820;DPVDBN=Nonaka_myopathy;DPVHGVS=NC_000009.12:g.36236828T>C	.