chr3:37048554:G>A Detail (hg19) (MLH1)

Information

Genome

Assembly Position
hg19 chr3:37,048,554-37,048,554
hg38 chr3:37,007,063-37,007,063 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000249.3:c.453G>A NP_000240.1:p.Thr151=
NM_001258273.1:c.-271G>A
NM_001258274.1:c.-271G>A
Summary

MGeND

Clinical significance Uncertain significance not provided
Variant entry 60
GWAS entry
Disease area statistics Show details

Frequency

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

Prediction

ClinVar

Clinical Significance Uncertain significance
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 tgv12068347 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Uncertain significance 2021/03/19 control germline MGS000047
(TMGS000111) 		Yukihide Momozawa
Koichi Matsuda		 RIKEN
The University of Tokyo
Uncertain significance 2021/03/19 Colorectal germline MGS000050
(TMGS000114) 		Yukihide Momozawa
Koichi Matsuda		 RIKEN
The University of Tokyo
Uncertain significance 2021/03/19 pancreatic germline MGS000051
(TMGS000115) 		Yukihide Momozawa
Koichi Matsuda		 RIKEN
The University of Tokyo
not provided pyloric antrum not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided descending colon not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided sigmoid colon not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided extrahepatic bile duct not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided ill-defined sites within the digestive system not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided bronchus or lung, unspecified not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Uncertain significance 2018-05-01 criteria provided, single submitter Lynch syndrome somatic Detail
Uncertain significance 2023-08-16 criteria provided, multiple submitters, no conflicts Hereditary cancer-predisposing syndrome germline Detail
Uncertain significance 2024-02-06 criteria provided, multiple submitters, no conflicts not specified germline Detail
Uncertain significance 2022-10-25 criteria provided, single submitter Hereditary nonpolyposis colorectal neoplasms germline Detail
Uncertain significance 2023-08-10 criteria provided, multiple submitters, no conflicts not provided germline unknown Detail
Uncertain significance 2018-06-13 reviewed by expert panel Lynch syndrome 1 germline Detail
Uncertain significance 2023-10-30 criteria provided, multiple submitters, no conflicts Colorectal cancer, hereditary nonpolyposis, type 2 germline unknown Detail
Uncertain significance 2021-03-03 criteria provided, single submitter Breast and/or ovarian cancer germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.121 Neoplastic Syndromes, Hereditary NA CLINVAR Detail
0.329 Hereditary Nonpolyposis Colorectal Cancer NA CLINVAR Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000249.4(MLH1):c.453G>A (p.Thr151=) AND Lynch syndrome ClinVar Detail
NM_000249.4(MLH1):c.453G>A (p.Thr151=) AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_000249.4(MLH1):c.453G>A (p.Thr151=) AND not specified ClinVar Detail
NM_000249.4(MLH1):c.453G>A (p.Thr151=) AND Hereditary nonpolyposis colorectal neoplasms ClinVar Detail
NM_000249.4(MLH1):c.453G>A (p.Thr151=) AND not provided ClinVar Detail
NM_000249.4(MLH1):c.453G>A (p.Thr151=) AND Lynch syndrome 1 ClinVar Detail
NM_000249.4(MLH1):c.453G>A (p.Thr151=) AND Colorectal cancer, hereditary nonpolyposis, type 2 ClinVar Detail
NM_000249.4(MLH1):c.453G>A (p.Thr151=) AND Breast and/or ovarian cancer ClinVar Detail
NA DisGeNET Detail
NA 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
rs369521379 dbSNP
Genome
hg19
Position
chr3:37,048,554-37,048,554
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1209
Mean of sample read depth (HGVD)
57.89
Standard deviation of sample read depth (HGVD)
30.91
Number of reference allele (HGVD)
2417
Number of alternative allele (HGVD)
1
Allele Frequency (HGVD)
4.1356492969396195E-4
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))
rs369521379
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0004
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
7
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8630
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)
121102
Allele Counts in All Race (ExAC)
1
Heterozygous Counts in All Race (ExAC)
1
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
8.257501940512956E-6
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