chr2:20003168:C>T Detail (hg38) (MATN3, WDR35-DT)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr2:20,202,929-20,202,929 View the variant detail on this assembly version. |
| hg38 | chr2:20,003,168-20,003,168 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_002381.4:c.909G>A | NP_002372.1:p.Thr303= |
| Ensemble | ENST00000407540.8:c.909G>A | ENST00000407540.8:p.Thr303= |
| ENST00000421259.2:c.791-1088G>A |
Summary
MGeND
| Clinical significance |
Benign
|
| Variant entry | 1 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.067 |
| ToMMo:0.070 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.031 |
Prediction
ClinVar
| Clinical Significance |
Benign
|
| Review star |  |
| Show details | |
Disease area statistics
MGeND
| Clinical significance | Last evaluated | Condition | Origin | Submission ID | Submitter | Institute | Citation | Comment | Image |
|---|---|---|---|---|---|---|---|---|---|
|
Benign
|
Centenarian |
germline
|
MGS000068
(TMGS000140) |
Kenjiro Kosaki | Keio University |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Benign
|
criteria provided, single submitter | not specified |
germline
|
Detail | |
|
Benign
|
2018-01-13 | criteria provided, single submitter | Multiple epiphyseal dysplasia type 5 |
germline
|
Detail |
|
Benign
|
2024-01-31 | criteria provided, multiple submitters, no conflicts | not provided |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_002381.5(MATN3):c.909G>A (p.Thr303=) AND not specified | ClinVar | Detail |
| NM_002381.5(MATN3):c.909G>A (p.Thr303=) AND Multiple epiphyseal dysplasia type 5 | ClinVar | Detail |
| NM_002381.5(MATN3):c.909G>A (p.Thr303=) AND not provided | 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
- rs28452699 dbSNP
- Genome
- hg38
- Position
- chr2:20,003,168-20,003,168
- Variant Type
- snv
- Reference Allele
- C
- Alternative Allele
- T
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 116.01
- Standard deviation of sample read depth (HGVD)
- 58.14
- Number of reference allele (HGVD)
- 2257
- Number of alternative allele (HGVD)
- 163
- Allele Frequency (HGVD)
- 0.06735537190082645
- Gene Symbol (HGVD)
- MATN3
- 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))
- rs28452699
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.07
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 1174
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8626
- East Asian Allele Counts (ExAC)
- 266
- East Asian Heterozygous Counts (ExAC)
- 254
- East Asian Homozygous Counts (ExAC)
- 6
- East Asian Allele Frequency (ExAC)
- 0.030837004405286344
- Chromosome Counts in All Race (ExAC)
- 120686
- Allele Counts in All Race (ExAC)
- 24444
- Heterozygous Counts in All Race (ExAC)
- 19036
- Homozygous Counts in All Race (ExAC)
- 2704
- Allele Frequency in All Race (ExAC)
- 0.20254213413320518
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