chr19:10291181:T>C Detail (hg19) (DNMT1)

Information

Genome

Assembly Position
hg19 chr19:10,291,181-10,291,181
hg38 chr19:10,180,505-10,180,505 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001318730.1:c.290A>G NP_001305659.1:p.His97Arg
NM_001379.3:c.290A>G NP_001370.1:p.His97Arg
NM_001130823.2:c.290A>G NP_001124295.1:p.His97Arg
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.178
ToMMo:0.175
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.207

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 126375 OMIM
HGNC 2976 HGNC
Ensembl ENSG00000130816 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv61156211 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2015-09-14 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2024-01-31 criteria provided, multiple submitters, no conflicts Hereditary sensory neuropathy-deafness-dementia syndrome germline Detail
Benign 2018-08-30 criteria provided, multiple submitters, no conflicts not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 azoospermia To explore the relationship between DNMT1 and spermatogenesis impairment, polymo... BeFree 24631383 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001130823.3(DNMT1):c.290A>G (p.His97Arg) AND not specified ClinVar Detail
NM_001130823.3(DNMT1):c.290A>G (p.His97Arg) AND Hereditary sensory neuropathy-deafness-dementia synd... ClinVar Detail
NM_001130823.3(DNMT1):c.290A>G (p.His97Arg) AND not provided ClinVar Detail
To explore the relationship between DNMT1 and spermatogenesis impairment, polymorphic distributions ... 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
rs16999593 dbSNP
Genome
hg19
Position
chr19:10,291,181-10,291,181
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
130.17
Standard deviation of sample read depth (HGVD)
59.53
Number of reference allele (HGVD)
1990
Number of alternative allele (HGVD)
430
Allele Frequency (HGVD)
0.17768595041322313
Gene Symbol (HGVD)
DNMT1
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))
rs16999593
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1749
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
2931
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8654
East Asian Allele Counts (ExAC)
1788
East Asian Heterozygous Counts (ExAC)
1410
East Asian Homozygous Counts (ExAC)
189
East Asian Allele Frequency (ExAC)
0.20660966027270627
Chromosome Counts in All Race (ExAC)
121412
Allele Counts in All Race (ExAC)
2637
Heterozygous Counts in All Race (ExAC)
2209
Homozygous Counts in All Race (ExAC)
214
Allele Frequency in All Race (ExAC)
0.021719434652258427
Genome browser