chr6:31960529:A>G Detail (hg38) (SKIC2)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr6:31,928,306-31,928,306 View the variant detail on this assembly version. |
| hg38 | chr6:31,960,529-31,960,529 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_006929.4:c.452A>G | NP_008860.4:p.Gln151Arg |
| Ensemble | ENST00000375394.7:c.452A>G | ENST00000375394.7:p.Gln151Arg |
| ENST00000491994.2:c.452A>G | ENST00000491994.2:p.Gln151Arg |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.087 |
| ToMMo:0.097 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.064 |
Prediction
ClinVar
| Clinical Significance |
Benign
Likely benign
|
| Review star |  |
| Show details | |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Benign
|
2018-03-06 | criteria provided, single submitter | trichohepatoenteric syndrome 2 |
germline
|
Detail |
|
Benign
Likely benign
|
2021-12-03 | criteria provided, multiple submitters, no conflicts | not specified |
germline
|
Detail |
|
Benign
|
2024-02-01 | criteria provided, single submitter | not provided |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.131 | age related macular degeneration | NA | GAD | Detail | |
| 0.125 | age related macular degeneration | NA | GAD | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_006929.5(SKIC2):c.452A>G (p.Gln151Arg) AND Trichohepatoenteric syndrome 2 | ClinVar | Detail |
| NM_006929.5(SKIC2):c.452A>G (p.Gln151Arg) AND not specified | ClinVar | Detail |
| NM_006929.5(SKIC2):c.452A>G (p.Gln151Arg) AND not provided | ClinVar | Detail |
| NA | DisGeNET | Detail |
| NA | 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
- rs438999 dbSNP
- Genome
- hg38
- Position
- chr6:31,960,529-31,960,529
- Variant Type
- snv
- Reference Allele
- A
- Alternative Allele
- G
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1172
- Mean of sample read depth (HGVD)
- 166.05
- Standard deviation of sample read depth (HGVD)
- 72.99
- Number of reference allele (HGVD)
- 2140
- Number of alternative allele (HGVD)
- 204
- Allele Frequency (HGVD)
- 0.08703071672354949
- Gene Symbol (HGVD)
- SKIV2L
- 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))
- rs438999
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0967
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 1620
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8648
- East Asian Allele Counts (ExAC)
- 552
- East Asian Heterozygous Counts (ExAC)
- 494
- East Asian Homozygous Counts (ExAC)
- 29
- East Asian Allele Frequency (ExAC)
- 0.06382978723404255
- Chromosome Counts in All Race (ExAC)
- 121322
- Allele Counts in All Race (ExAC)
- 12104
- Heterozygous Counts in All Race (ExAC)
- 10610
- Homozygous Counts in All Race (ExAC)
- 747
- Allele Frequency in All Race (ExAC)
- 0.09976756070621981
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