chr15:28228553:C>T Detail (hg19) (OCA2)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr15:28,228,553-28,228,553 |
| hg38 | chr15:27,983,407-27,983,407 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_000275.2:c.1441G>A | NP_000266.2:p.Ala481Thr |
| NM_001300984.1:c.1369G>A | NP_001287913.1:p.Ala457Thr | |
| Ensemble | ENST00000354638.8:c.1441G>A | ENST00000354638.8:p.Ala481Thr |
Summary
MGeND
| Clinical significance |
Likely benign
Likely pathogenic
|
| Variant entry | 3 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.066 |
| ToMMo:0.087 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.030 |
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 |
|---|---|---|---|---|---|---|---|---|---|
|
Likely pathogenic
|
other |
germline
|
MGS000001
(TMGS000137) |
Kenjiro Kosaki | Keio University | ||||
|
Likely benign
|
oculocutaneous albinism type 2 |
germline
|
MGS000082
(TMGS000165) |
Kenjiro Kosaki Kenjiro Kosaki |
Keio University Mutation View |
||||
|
Likely benign
|
Angelman syndrome |
germline
|
MGS000082
(TMGS000165) |
Kenjiro Kosaki Kenjiro Kosaki |
Keio University Mutation View |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
Conflicting interpretations of pathogenicity
|
2022-07-12 | criteria provided, conflicting interpretations | Tyrosinase-positive oculocutaneous albinism |
germline
unknown
|
Detail |
|
Likely benign
|
2023-02-14 | criteria provided, multiple submitters, no conflicts | not specified |
germline
|
Detail |
Benign
|
2024-02-01 | criteria provided, multiple submitters, no conflicts | not provided |
germline
|
Detail |
|
Likely benign
|
2023-04-21 | criteria provided, single submitter | OCA2-related disorder |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.563 | Oculocutaneous albinism type 2 | NA | CLINVAR | Detail | |
| 0.563 | Oculocutaneous albinism type 2 | Six novel P gene mutations and oculocutaneous albinism type 2 frequency in Japan... | UNIPROT | 12713581 | Detail |
| <0.001 | actinic keratosis | Another non-synonymous variant, A481T in OCA2, was associated with the risk of s... | BeFree | 24617981 | Detail |
| 0.003 | squamous cell carcinoma | Another non-synonymous variant, A481T in OCA2, was associated with the risk of s... | BeFree | 24617981 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_000275.3(OCA2):c.1441G>A (p.Ala481Thr) AND Tyrosinase-positive oculocutaneous albinism | ClinVar | Detail |
| NM_000275.3(OCA2):c.1441G>A (p.Ala481Thr) AND not specified | ClinVar | Detail |
| NM_000275.3(OCA2):c.1441G>A (p.Ala481Thr) AND not provided | ClinVar | Detail |
| NM_000275.3(OCA2):c.1441G>A (p.Ala481Thr) AND OCA2-related disorder | ClinVar | Detail |
| NA | DisGeNET | Detail |
| Six novel P gene mutations and oculocutaneous albinism type 2 frequency in Japanese albino patients. | DisGeNET | Detail |
| Another non-synonymous variant, A481T in OCA2, was associated with the risk of squamous cell carcino... | DisGeNET | Detail |
| Another non-synonymous variant, A481T in OCA2, was associated with the risk of squamous cell carcino... | 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
- rs74653330 dbSNP
- Genome
- hg19
- Position
- chr15:28,228,553-28,228,553
- Variant Type
- snv
- Reference Allele
- C
- Alternative Allele
- T
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 203.88
- Standard deviation of sample read depth (HGVD)
- 87.80
- Number of reference allele (HGVD)
- 2260
- Number of alternative allele (HGVD)
- 160
- Allele Frequency (HGVD)
- 0.06611570247933884
- Gene Symbol (HGVD)
- OCA2
- 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))
- rs74653330
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0869
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 1457
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8654
- East Asian Allele Counts (ExAC)
- 262
- East Asian Heterozygous Counts (ExAC)
- 244
- East Asian Homozygous Counts (ExAC)
- 9
- East Asian Allele Frequency (ExAC)
- 0.030275017333025192
- Chromosome Counts in All Race (ExAC)
- 121408
- Allele Counts in All Race (ExAC)
- 941
- Heterozygous Counts in All Race (ExAC)
- 901
- Homozygous Counts in All Race (ExAC)
- 20
- Allele Frequency in All Race (ExAC)
- 0.0077507248286768585
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