chr19:10162696:T>C Detail (hg38) (DNMT1)

Information

Genome

Assembly Position
hg19 chr19:10,273,372-10,273,372 View the variant detail on this assembly version.
hg38 chr19:10,162,696-10,162,696

HGVS

Type Transcript Protein
RefSeq NM_001318730.1:c.931A>G NP_001305659.1:p.Ile311Val
NM_001379.3:c.931A>G NP_001370.1:p.Ile311Val
NM_001130823.2:c.979A>G NP_001124295.1:p.Ile327Val
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.338
ToMMo:0.331
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.422

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 tgv61155484 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2015-09-22 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts Hereditary sensory neuropathy-deafness-dementia syndrome 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
0.004 colon carcinoma However, statistically significant interactions modifying CC risk were observed ... BeFree 22961839 Detail
0.003 Malignant tumor of colon However, statistically significant interactions modifying CC risk were observed ... BeFree 22961839 Detail
<0.001 colon carcinoma However, statistically significant interactions modifying CC risk were observed ... BeFree 22961839 Detail
<0.001 Malignant tumor of colon However, statistically significant interactions modifying CC risk were observed ... BeFree 22961839 Detail
<0.001 Malignant neoplasm of esophagus There was an inverse association between DNMT1 rs2228612 and esophageal cancer (... BeFree 25337902 Detail
<0.001 Esophageal Neoplasms There was an inverse association between DNMT1 rs2228612 and esophageal cancer (... BeFree 25337902 Detail
<0.001 esophageal carcinoma There was an inverse association between DNMT1 rs2228612 and esophageal cancer (... BeFree 25337902 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001130823.3(DNMT1):c.979A>G (p.Ile327Val) AND not specified ClinVar Detail
NM_001130823.3(DNMT1):c.979A>G (p.Ile327Val) AND Hereditary sensory neuropathy-deafness-dementia syn... ClinVar Detail
To explore the relationship between DNMT1 and spermatogenesis impairment, polymorphic distributions ... DisGeNET Detail
However, statistically significant interactions modifying CC risk were observed for DNMT1 I311V with... DisGeNET Detail
However, statistically significant interactions modifying CC risk were observed for DNMT1 I311V with... DisGeNET Detail
However, statistically significant interactions modifying CC risk were observed for DNMT1 I311V with... DisGeNET Detail
However, statistically significant interactions modifying CC risk were observed for DNMT1 I311V with... DisGeNET Detail
There was an inverse association between DNMT1 rs2228612 and esophageal cancer (any G versus A/A, SB... DisGeNET Detail
There was an inverse association between DNMT1 rs2228612 and esophageal cancer (any G versus A/A, SB... DisGeNET Detail
There was an inverse association between DNMT1 rs2228612 and esophageal cancer (any G versus A/A, SB... 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
rs2228612 dbSNP
Genome
hg38
Position
chr19:10,162,696-10,162,696
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1182
Mean of sample read depth (HGVD)
41.51
Standard deviation of sample read depth (HGVD)
32.09
Number of reference allele (HGVD)
1565
Number of alternative allele (HGVD)
799
Allele Frequency (HGVD)
0.3379864636209814
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))
rs2228612
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.3313
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
5551
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16756
East Asian Chromosome Counts (ExAC)
8622
East Asian Allele Counts (ExAC)
3635
East Asian Heterozygous Counts (ExAC)
2089
East Asian Homozygous Counts (ExAC)
773
East Asian Allele Frequency (ExAC)
0.4215959174205521
Chromosome Counts in All Race (ExAC)
121254
Allele Counts in All Race (ExAC)
16001
Heterozygous Counts in All Race (ExAC)
12491
Homozygous Counts in All Race (ExAC)
1755
Allele Frequency in All Race (ExAC)
0.13196265690204034
Genome browser