chr2:47795968:C>T Detail (hg38) (MSH6, FBXO11)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr2:48,023,107-48,023,107 View the variant detail on this assembly version. |
| hg38 | chr2:47,795,968-47,795,968 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | ||
| Ensemble | ENST00000405808.5:c.170-6528G>A |
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_000179.2:c.532C>T | NP_000170.1:p.Arg178Cys |
| NM_001281492.1:c.238-2643C>T | ||
| Ensemble | ENST00000234420.11:c.532C>T | ENST00000234420.11:p.Arg178Cys |
Summary
MGeND
| Clinical significance |
Benign
other
|
| Variant entry | 2 |
| 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:[No Data.] |
Prediction
ClinVar
| Clinical Significance | Conflicting classifications of pathogenicity |
| Review star |  |
| Show details | |
Disease area statistics
MGeND
| Clinical significance | Last evaluated | Condition | Origin | Submission ID | Submitter | Institute | Citation | Comment | Image |
|---|---|---|---|---|---|---|---|---|---|
|
other
|
2018/02/22 | Ovarian cancer |
germline
|
MGS000017
(TMGS000052) |
Kohei Miyazono | Tokyo University | |||
|
Benign
|
Centenarian |
germline
|
MGS000068
(TMGS000140) |
Kenjiro Kosaki | Keio University |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
Uncertain significance
|
2023-08-24 | criteria provided, multiple submitters, no conflicts | not provided |
germline
unknown
|
Detail |
Conflicting interpretations of pathogenicity
|
2023-10-25 | criteria provided, conflicting interpretations | Hereditary cancer-predisposing syndrome |
germline
|
Detail |
|
Benign
|
2024-01-10 | criteria provided, single submitter | Hereditary nonpolyposis colorectal neoplasms |
germline
|
Detail |
|
Uncertain significance
|
2018-11-23 | criteria provided, single submitter | not specified |
germline
|
Detail |
|
Uncertain significance
|
2019-05-28 | criteria provided, single submitter | Lynch syndrome 5 |
unknown
|
Detail |
|
Uncertain significance
|
2019-05-01 | criteria provided, single submitter | hereditary breast ovarian cancer syndrome |
germline
|
Detail |
|
Uncertain significance
|
2023-10-19 | criteria provided, single submitter | endometrial carcinoma |
unknown
|
Detail |
|
Uncertain significance
|
2023-12-18 | criteria provided, single submitter | Lynch syndrome |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_000179.3(MSH6):c.532C>T (p.Arg178Cys) AND not provided | ClinVar | Detail |
| NM_000179.3(MSH6):c.532C>T (p.Arg178Cys) AND Hereditary cancer-predisposing syndrome | ClinVar | Detail |
| NM_000179.3(MSH6):c.532C>T (p.Arg178Cys) AND Hereditary nonpolyposis colorectal neoplasms | ClinVar | Detail |
| NM_000179.3(MSH6):c.532C>T (p.Arg178Cys) AND not specified | ClinVar | Detail |
| NM_000179.3(MSH6):c.532C>T (p.Arg178Cys) AND Lynch syndrome 5 | ClinVar | Detail |
| NM_000179.3(MSH6):c.532C>T (p.Arg178Cys) AND Hereditary breast ovarian cancer syndrome | ClinVar | Detail |
| NM_000179.3(MSH6):c.532C>T (p.Arg178Cys) AND Endometrial carcinoma | ClinVar | Detail |
| NM_000179.3(MSH6):c.532C>T (p.Arg178Cys) AND Lynch syndrome | ClinVar | 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
- rs730881813 dbSNP
- Genome
- hg38
- Position
- chr2:47,795,968-47,795,968
- Variant Type
- snv
- Reference Allele
- C
- Alternative Allele
- T
- Filtering Status (HGVD)
- PASS
- Filtering Status (HGVD)
- LowQual
- # of samples (HGVD)
- 1195
- Mean of sample read depth (HGVD)
- 39.62
- Standard deviation of sample read depth (HGVD)
- 19.66
- Number of reference allele (HGVD)
- 2389
- Number of alternative allele (HGVD)
- 1
- Allele Frequency (HGVD)
- 4.1841004184100416E-4
- Gene Symbol (HGVD)
- MSH6
- 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))
- rs730881813
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0008
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 13
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
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