chr3:37067120:T>A Detail (hg19) (MLH1)

Information

Genome

Assembly Position
hg19 chr3:37,067,120-37,067,120
hg38 chr3:37,025,629-37,025,629 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001258273.1:c.316-8T>A
NM_001167619.1:c.316-8T>A
NM_001258271.1:c.1039-8T>A
Summary

MGeND

Clinical significance Benign
Variant entry 39
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.012
ToMMo:0.014
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:<0.001

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 tgv12069409 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Benign 2020/04/20 lower third of oesophagus not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 oesophagus, unspecified not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 fundus of stomach not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 stomach, unspecified not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 ileum not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 caecum not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 transverse colon not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 descending colon not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 sigmoid colon not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 colon, unspecified not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 liver cell carcinoma not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 head of pancreas not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 body of pancreas not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 ill-defined sites within the digestive system not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 bronchus or lung, unspecified not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2011-12-22 no assertion criteria provided Lynch syndrome germline Detail
Benign 2018-07-06 criteria provided, multiple submitters, no conflicts not specified germline unknown Detail
Benign 2020-03-22 criteria provided, multiple submitters, no conflicts Hereditary cancer-predisposing syndrome germline Detail
Benign 2016-04-20 reviewed by expert panel Lynch syndrome 1 germline Detail
Benign 2024-02-01 criteria provided, single submitter Hereditary nonpolyposis colorectal neoplasms germline Detail
Conflicting interpretations of pathogenicity 2019-05-28 criteria provided, conflicting interpretations Colorectal cancer, hereditary nonpolyposis, type 2 germline unknown Detail
Benign no assertion criteria provided endometrial carcinoma unknown Detail
Benign 2019-05-01 criteria provided, single submitter Breast and/or ovarian cancer germline Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_000249.4(MLH1):c.1039-8T>A AND Lynch syndrome ClinVar Detail
NM_000249.4(MLH1):c.1039-8T>A AND not specified ClinVar Detail
NM_000249.4(MLH1):c.1039-8T>A AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_000249.4(MLH1):c.1039-8T>A AND Lynch syndrome 1 ClinVar Detail
NM_000249.4(MLH1):c.1039-8T>A AND Hereditary nonpolyposis colorectal neoplasms ClinVar Detail
NM_000249.4(MLH1):c.1039-8T>A AND Colorectal cancer, hereditary nonpolyposis, type 2 ClinVar Detail
NM_000249.4(MLH1):c.1039-8T>A AND Endometrial carcinoma ClinVar Detail
NM_000249.4(MLH1):c.1039-8T>A AND Breast and/or ovarian cancer ClinVar Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs193922367 dbSNP
Genome
hg19
Position
chr3:37,067,120-37,067,120
Variant Type
snv
Reference Allele
T
Alternative Allele
A
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
VQSRTrancheSNP99.00to99.90
# of samples (HGVD)
998
Mean of sample read depth (HGVD)
28.11
Standard deviation of sample read depth (HGVD)
13.70
Number of reference allele (HGVD)
1790
Number of alternative allele (HGVD)
22
Allele Frequency (HGVD)
0.012141280353200883
Gene Symbol (HGVD)
MLH1
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))
rs193922367
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0136
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
227
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16742
East Asian Chromosome Counts (ExAC)
2738
East Asian Allele Counts (ExAC)
0
East Asian Heterozygous Counts (ExAC)
0
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.0
Chromosome Counts in All Race (ExAC)
43560
Allele Counts in All Race (ExAC)
6
Heterozygous Counts in All Race (ExAC)
6
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
1.377410468319559E-4
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