chr2:219425727:C>T Detail (hg38) (DES)

Information

Genome

Assembly Position
hg19 chr2:220,290,449-220,290,449 View the variant detail on this assembly version.
hg38 chr2:219,425,727-219,425,727

HGVS

Type Transcript Protein
RefSeq NM_001927.3:c.1353C>T NP_001918.3:p.Ile451=
Ensemble ENST00000373960.4:c.1353C>T ENST00000373960.4:p.Ile451=
Summary

MGeND

Clinical significance Benign
Variant entry 1
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:<0.001
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.011

Prediction

ClinVar

Clinical Significance Conflicting classifications of pathogenicity
Review star
Show details
Links
Type Database ID Link
Gene MIM 125660 OMIM
HGNC 2770 HGNC
Ensembl ENSG00000175084 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv10570821 TogoVar
COSMIC COSM4464813 COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Benign Centenarian germline MGS000068
(TMGS000140) 		Kenjiro Kosaki Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2015-10-01 criteria provided, single submitter not specified germline Detail
Likely benign 2017-04-10 criteria provided, single submitter germline Detail
Conflicting interpretations of pathogenicity 2015-09-10 criteria provided, conflicting interpretations not provided germline Detail
Benign 2024-01-24 criteria provided, single submitter Desmin-related myofibrillar myopathy germline Detail
Benign 2021-05-03 criteria provided, single submitter cardiomyopathy germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.440 CARDIOMYOPATHY, DILATED, 1I NA CLINVAR Detail
0.440 CARDIOMYOPATHY, DILATED, 1I Desmin mutation responsible for idiopathic dilated cardiomyopathy. UNIPROT 10430757 Detail
0.564 MYOPATHY, MYOFIBRILLAR, DESMIN-RELATED Desmin mutation responsible for idiopathic dilated cardiomyopathy. UNIPROT 10430757 Detail
0.137 Cardiomyopathy, Dilated The missense mutation (Ile451Met) of the desmin gene can be the genetic cause of... BeFree 11728149 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001927.4(DES):c.1353C>T (p.Ile451=) AND not specified ClinVar Detail
NM_001927.4(DES):c.1353C>T (p.Ile451=) AND Cardiovascular phenotype ClinVar Detail
NM_001927.4(DES):c.1353C>T (p.Ile451=) AND not provided ClinVar Detail
NM_001927.4(DES):c.1353C>T (p.Ile451=) AND Desmin-related myofibrillar myopathy ClinVar Detail
NM_001927.4(DES):c.1353C>T (p.Ile451=) AND Cardiomyopathy ClinVar Detail
NA DisGeNET Detail
Desmin mutation responsible for idiopathic dilated cardiomyopathy. DisGeNET Detail
Desmin mutation responsible for idiopathic dilated cardiomyopathy. DisGeNET Detail
The missense mutation (Ile451Met) of the desmin gene can be the genetic cause of dilated cardiomyopa... DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs121913002 dbSNP
Genome
hg38
Position
chr2:219,425,727-219,425,727
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1208
Mean of sample read depth (HGVD)
71.71
Standard deviation of sample read depth (HGVD)
32.72
Number of reference allele (HGVD)
2414
Number of alternative allele (HGVD)
2
Allele Frequency (HGVD)
8.278145695364238E-4
Gene Symbol (HGVD)
DES
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs121913002
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0004
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
6
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
3920
East Asian Allele Counts (ExAC)
43
East Asian Heterozygous Counts (ExAC)
43
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.01096938775510204
Chromosome Counts in All Race (ExAC)
56434
Allele Counts in All Race (ExAC)
48
Heterozygous Counts in All Race (ExAC)
48
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
8.505510862246164E-4
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