chr5:80168937:G>A Detail (hg19) (MSH3)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr5:80,168,937-80,168,937 |
| hg38 | chr5:80,873,118-80,873,118 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_002439.4:c.3133G>A | NP_002430.3:p.Ala1045Thr |
| Ensemble | ENST00000265081.7:c.3133G>A | ENST00000265081.7:p.Ala1045Thr |
| ENST00000658259.1:c.2965G>A | ENST00000658259.1:p.Ala989Thr |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.769 |
| ToMMo:0.753 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.744 |
Prediction
ClinVar
| Clinical Significance |
Benign
|
| Review star |  |
| Show details | |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Benign
|
2021-02-27 | criteria provided, multiple submitters, no conflicts | Hereditary cancer-predisposing syndrome |
germline
|
Detail |
|
Benign
|
2024-02-01 | criteria provided, multiple submitters, no conflicts | not provided |
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>A) polym... | BeFree | 19781088 | Detail |
| 0.004 | breast carcinoma | Using unconditional logistic regression we found that MLH3 (L844P, G>A) polym... | BeFree | 19781088 | Detail |
| 0.013 | Malignant neoplasm of breast | Using unconditional logistic regression we found that MLH3 (L844P, G>A) polym... | BeFree | 19781088 | Detail |
| 0.003 | Malignant neoplasm of breast | Using unconditional logistic regression we found that MLH3 (L844P, G>A) polym... | BeFree | 19781088 | Detail |
| 0.008 | breast carcinoma | Using unconditional logistic regression we found that MLH3 (L844P, G>A) polym... | BeFree | 19781088 | Detail |
| <0.001 | breast carcinoma | Using unconditional logistic regression we found that MLH3 (L844P, G>A) polym... | BeFree | 19781088 | Detail |
| <0.001 | Malignant neoplasm of breast | Using unconditional logistic regression we found that MLH3 (L844P, G>A) polym... | BeFree | 19781088 | Detail |
| 0.015 | Malignant neoplasm of breast | Using unconditional logistic regression we found that MLH3 (L844P, G>A) polym... | BeFree | 19781088 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_002439.5(MSH3):c.3133G>A (p.Ala1045Thr) AND Hereditary cancer-predisposing syndrome | ClinVar | Detail |
| NM_002439.5(MSH3):c.3133G>A (p.Ala1045Thr) AND not provided | ClinVar | Detail |
| Using unconditional logistic regression we found that MLH3 (L844P, G>A) polymorphism GA (Leu/Pro)... | DisGeNET | Detail |
| Using unconditional logistic regression we found that MLH3 (L844P, G>A) polymorphism GA (Leu/Pro)... | DisGeNET | Detail |
| Using unconditional logistic regression we found that MLH3 (L844P, G>A) polymorphism GA (Leu/Pro)... | DisGeNET | Detail |
| Using unconditional logistic regression we found that MLH3 (L844P, G>A) polymorphism GA (Leu/Pro)... | DisGeNET | Detail |
| Using unconditional logistic regression we found that MLH3 (L844P, G>A) polymorphism GA (Leu/Pro)... | DisGeNET | Detail |
| Using unconditional logistic regression we found that MLH3 (L844P, G>A) polymorphism GA (Leu/Pro)... | DisGeNET | Detail |
| Using unconditional logistic regression we found that MLH3 (L844P, G>A) polymorphism GA (Leu/Pro)... | DisGeNET | Detail |
| Using unconditional logistic regression we found that MLH3 (L844P, G>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
- -
- dbSNP
- rs26279 dbSNP
- Genome
- hg19
- Position
- chr5:80,168,937-80,168,937
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- A
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 170.56
- Standard deviation of sample read depth (HGVD)
- 70.91
- Number of reference allele (HGVD)
- 558
- Number of alternative allele (HGVD)
- 1862
- Allele Frequency (HGVD)
- 0.7694214876033058
- Gene Symbol (HGVD)
- MSH3
- 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))
- rs26279
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.7532
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 12624
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8644
- East Asian Allele Counts (ExAC)
- 6429
- East Asian Heterozygous Counts (ExAC)
- 1641
- East Asian Homozygous Counts (ExAC)
- 2394
- East Asian Allele Frequency (ExAC)
- 0.7437528921795465
- Chromosome Counts in All Race (ExAC)
- 121342
- Allele Counts in All Race (ExAC)
- 88636
- Heterozygous Counts in All Race (ExAC)
- 23722
- Homozygous Counts in All Race (ExAC)
- 32457
- Allele Frequency in All Race (ExAC)
- 0.7304643074945196
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