chr3:37016100:C>T Detail (hg38) (MLH1)

Information

Genome

Assembly Position
hg19 chr3:37,057,591-37,057,591 View the variant detail on this assembly version.
hg38 chr3:37,016,100-37,016,100

HGVS

Type Transcript Protein
RefSeq NM_000249.3:c.791-1406C>T
NM_001167617.1:c.497-1406C>T
NM_001167618.1:c.68-1406C>T
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.158
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:[No Data.]

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 120436 OMIM
HGNC 7127 HGNC
Ensembl ENSG00000076242 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv12068899 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2013-09-05 reviewed by expert panel Lynch syndrome germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 oligospermia One intronic SNP in MLH1 (rs4647269) and two non-synonymous SNPs in PMS2 (rs1059... BeFree 22594646 Detail
<0.001 azoospermia One intronic SNP in MLH1 (rs4647269) and two non-synonymous SNPs in PMS2 (rs1059... BeFree 22594646 Detail
0.005 azoospermia One intronic SNP in MLH1 (rs4647269) and two non-synonymous SNPs in PMS2 (rs1059... BeFree 22594646 Detail
0.003 oligospermia One intronic SNP in MLH1 (rs4647269) and two non-synonymous SNPs in PMS2 (rs1059... BeFree 22594646 Detail
<0.001 azoospermia One intronic SNP in MLH1 (rs4647269) and two non-synonymous SNPs in PMS2 (rs1059... BeFree 22594646 Detail
<0.001 oligospermia One intronic SNP in MLH1 (rs4647269) and two non-synonymous SNPs in PMS2 (rs1059... BeFree 22594646 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000249.4(MLH1):c.791-1406C>T AND Lynch syndrome ClinVar Detail
One intronic SNP in MLH1 (rs4647269) and two non-synonymous SNPs in PMS2 (rs1059060, Ser775Asn) and ... DisGeNET Detail
One intronic SNP in MLH1 (rs4647269) and two non-synonymous SNPs in PMS2 (rs1059060, Ser775Asn) and ... DisGeNET Detail
One intronic SNP in MLH1 (rs4647269) and two non-synonymous SNPs in PMS2 (rs1059060, Ser775Asn) and ... DisGeNET Detail
One intronic SNP in MLH1 (rs4647269) and two non-synonymous SNPs in PMS2 (rs1059060, Ser775Asn) and ... DisGeNET Detail
One intronic SNP in MLH1 (rs4647269) and two non-synonymous SNPs in PMS2 (rs1059060, Ser775Asn) and ... DisGeNET Detail
One intronic SNP in MLH1 (rs4647269) and two non-synonymous SNPs in PMS2 (rs1059060, Ser775Asn) and ... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs4647269 dbSNP
Genome
hg38
Position
chr3:37,016,100-37,016,100
Variant Type
snv
Reference Allele
C
Alternative Allele
T
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))
rs4647269
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1578
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
2645
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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