chr1:75803775:G>A Detail (hg38) (MSH4)

Information

Genome

Assembly Position
hg19 chr1:76,269,460-76,269,460 View the variant detail on this assembly version.
hg38 chr1:75,803,775-75,803,775

HGVS

Type Transcript Protein
RefSeq NM_002440.3:c.289G>A NP_002431.2:p.Ala97Thr
Ensemble ENST00000263187.4:c.289G>A ENST00000263187.4:p.Ala97Thr
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.051
ToMMo:0.058
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.020

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 602105 OMIM
HGNC 7327 HGNC
Ensembl ENSG00000057468 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv2030061 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2023-04-11 criteria provided, single submitter spermatogenic failure 2 germline Detail
Benign 2023-04-11 criteria provided, single submitter Premature ovarian failure 20 germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 breast carcinoma Using unconditional logistic regression we found that MLH3 (L844P, G&gt;A) polym... BeFree 19781088 Detail
0.004 breast carcinoma Using unconditional logistic regression we found that MLH3 (L844P, G&gt;A) polym... BeFree 19781088 Detail
0.013 Malignant neoplasm of breast Using unconditional logistic regression we found that MLH3 (L844P, G&gt;A) polym... BeFree 19781088 Detail
0.003 Malignant neoplasm of breast Using unconditional logistic regression we found that MLH3 (L844P, G&gt;A) polym... BeFree 19781088 Detail
0.008 breast carcinoma Using unconditional logistic regression we found that MLH3 (L844P, G&gt;A) polym... BeFree 19781088 Detail
<0.001 breast carcinoma Using unconditional logistic regression we found that MLH3 (L844P, G&gt;A) polym... BeFree 19781088 Detail
<0.001 Malignant neoplasm of breast Using unconditional logistic regression we found that MLH3 (L844P, G&gt;A) polym... BeFree 19781088 Detail
0.015 Malignant neoplasm of breast Using unconditional logistic regression we found that MLH3 (L844P, G&gt;A) polym... BeFree 19781088 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_002440.4(MSH4):c.289G>A (p.Ala97Thr) AND Spermatogenic failure 2 ClinVar Detail
NM_002440.4(MSH4):c.289G>A (p.Ala97Thr) AND Premature ovarian failure 20 ClinVar Detail
Using unconditional logistic regression we found that MLH3 (L844P, G&gt;A) polymorphism GA (Leu/Pro)... DisGeNET Detail
Using unconditional logistic regression we found that MLH3 (L844P, G&gt;A) polymorphism GA (Leu/Pro)... DisGeNET Detail
Using unconditional logistic regression we found that MLH3 (L844P, G&gt;A) polymorphism GA (Leu/Pro)... DisGeNET Detail
Using unconditional logistic regression we found that MLH3 (L844P, G&gt;A) polymorphism GA (Leu/Pro)... DisGeNET Detail
Using unconditional logistic regression we found that MLH3 (L844P, G&gt;A) polymorphism GA (Leu/Pro)... DisGeNET Detail
Using unconditional logistic regression we found that MLH3 (L844P, G&gt;A) polymorphism GA (Leu/Pro)... DisGeNET Detail
Using unconditional logistic regression we found that MLH3 (L844P, G&gt;A) polymorphism GA (Leu/Pro)... DisGeNET Detail
Using unconditional logistic regression we found that MLH3 (L844P, G&gt;A) polymorphism GA (Leu/Pro)... 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
-
Genome
hg38
Position
chr1:75,803,775-75,803,775
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
63.25
Standard deviation of sample read depth (HGVD)
27.39
Number of reference allele (HGVD)
2297
Number of alternative allele (HGVD)
123
Allele Frequency (HGVD)
0.050826446280991734
Gene Symbol (HGVD)
MSH4
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))
rs5745325
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0585
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
980
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8640
East Asian Allele Counts (ExAC)
175
East Asian Heterozygous Counts (ExAC)
171
East Asian Homozygous Counts (ExAC)
2
East Asian Allele Frequency (ExAC)
0.02025462962962963
Chromosome Counts in All Race (ExAC)
120590
Allele Counts in All Race (ExAC)
31769
Heterozygous Counts in All Race (ExAC)
22463
Homozygous Counts in All Race (ExAC)
4653
Allele Frequency in All Race (ExAC)
0.26344638858943525
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