chr19:10156401:T>C Detail (hg38) (DNMT1)

Information

Genome

Assembly Position
hg19 chr19:10,267,077-10,267,077 View the variant detail on this assembly version.
hg38 chr19:10,156,401-10,156,401

HGVS

Type Transcript Protein
RefSeq NM_001318730.1:c.1341A>G NP_001305659.1:p.Pro447=
NM_001379.3:c.1341A>G NP_001370.1:p.Pro447=
NM_001130823.2:c.1389A>G NP_001124295.1:p.Pro463=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.576
ToMMo:0.557
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.693

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 tgv61155169 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign criteria provided, single submitter not specified germline Detail
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts Hereditary sensory neuropathy-deafness-dementia syndrome germline Detail
Benign 2015-03-03 criteria provided, single submitter not provided germline Detail
Benign 2021-07-30 criteria provided, single submitter autosomal dominant cerebellar ataxia, deafness and narcolepsy 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.1389A>G (p.Pro463=) AND not specified ClinVar Detail
NM_001130823.3(DNMT1):c.1389A>G (p.Pro463=) AND Hereditary sensory neuropathy-deafness-dementia synd... ClinVar Detail
NM_001130823.3(DNMT1):c.1389A>G (p.Pro463=) AND not provided ClinVar Detail
NM_001130823.3(DNMT1):c.1389A>G (p.Pro463=) AND Autosomal dominant cerebellar ataxia, deafness and n... 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
rs2228611 dbSNP
Genome
hg38
Position
chr19:10,156,401-10,156,401
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
48.30
Standard deviation of sample read depth (HGVD)
24.75
Number of reference allele (HGVD)
1027
Number of alternative allele (HGVD)
1393
Allele Frequency (HGVD)
0.5756198347107438
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))
rs2228611
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.5565
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
9327
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8634
East Asian Allele Counts (ExAC)
5984
East Asian Heterozygous Counts (ExAC)
1806
East Asian Homozygous Counts (ExAC)
2089
East Asian Allele Frequency (ExAC)
0.6930738939078064
Chromosome Counts in All Race (ExAC)
121254
Allele Counts in All Race (ExAC)
62902
Heterozygous Counts in All Race (ExAC)
29794
Homozygous Counts in All Race (ExAC)
16554
Allele Frequency in All Race (ExAC)
0.5187622676365315
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