chr22:50625611:G>C Detail (hg38) (ARSA)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr22:51,064,039-51,064,039 View the variant detail on this assembly version. |
| hg38 | chr22:50,625,611-50,625,611 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_000487.5:c.1178C>G | NP_000478.3:p.Thr393Ser |
| NM_001085426.2:c.1178C>G | NP_001078895.2:p.Thr393Ser | |
| NM_001085427.2:c.1178C>G | NP_001078896.2:p.Thr393Ser |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.400 |
| ToMMo:0.410 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.298 |
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
|
2024-02-01 | criteria provided, multiple submitters, no conflicts | metachromatic leukodystrophy |
germline
not applicable
unknown
|
Detail |
|
Benign
|
2015-03-16 | criteria provided, multiple submitters, no conflicts | not specified |
germline
|
Detail |
|
Benign
|
2015-03-03 | criteria provided, single submitter | not provided |
germline
unknown
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.514 | Leukodystrophy, Metachromatic | NA | CLINVAR | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_000487.6(ARSA):c.1178C>G (p.Thr393Ser) AND Metachromatic leukodystrophy | ClinVar | Detail |
| NM_000487.6(ARSA):c.1178C>G (p.Thr393Ser) AND not specified | ClinVar | Detail |
| NM_000487.6(ARSA):c.1178C>G (p.Thr393Ser) AND not provided | ClinVar | 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
- rs743616 dbSNP
- Genome
- hg38
- Position
- chr22:50,625,611-50,625,611
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- C
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1151
- Mean of sample read depth (HGVD)
- 28.14
- Standard deviation of sample read depth (HGVD)
- 18.70
- Number of reference allele (HGVD)
- 1382
- Number of alternative allele (HGVD)
- 920
- Allele Frequency (HGVD)
- 0.3996524761077324
- Gene Symbol (HGVD)
- ARSA
- 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))
- rs743616
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.4105
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 6876
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16752
- East Asian Chromosome Counts (ExAC)
- 8614
- East Asian Allele Counts (ExAC)
- 2570
- East Asian Heterozygous Counts (ExAC)
- 1822
- East Asian Homozygous Counts (ExAC)
- 374
- East Asian Allele Frequency (ExAC)
- 0.2983515207801254
- Chromosome Counts in All Race (ExAC)
- 120940
- Allele Counts in All Race (ExAC)
- 58572
- Heterozygous Counts in All Race (ExAC)
- 29102
- Homozygous Counts in All Race (ExAC)
- 14735
- Allele Frequency in All Race (ExAC)
- 0.4843062675706962
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