chr1:115220086:C>T Detail (hg19) (AMPD1)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr1:115,220,086-115,220,086 |
| hg38 | chr1:114,677,465-114,677,465 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_000036.2:c.1274G>A | NP_000027.2:p.Arg425His |
| NM_001172626.1:c.1262G>A | NP_001166097.1:p.Arg421His | |
| Ensemble | ENST00000520113.7:c.1274G>A | ENST00000520113.7:p.Arg425His |
Summary
MGeND
| Clinical significance |
Benign
|
| Variant entry | 1 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.004 |
| ToMMo:0.004 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.011 |
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 |
|---|---|---|---|---|---|---|---|---|---|
|
Benign
|
Centenarian |
germline
|
MGS000068
(TMGS000140) |
Kenjiro Kosaki | Keio University |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
Conflicting interpretations of pathogenicity
|
2024-01-10 | criteria provided, conflicting interpretations | Muscle AMP deaminase deficiency |
germline
|
Detail |
Uncertain significance
|
2014-11-10 | criteria provided, single submitter | not provided |
germline
|
Detail |
|
Uncertain significance
|
2022-05-04 | criteria provided, single submitter | not specified |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.241 | Muscle AMP deaminase deficiency | NA | CLINVAR | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_000036.3(AMPD1):c.1274G>A (p.Arg425His) AND Muscle AMP deaminase deficiency | ClinVar | Detail |
| NM_000036.3(AMPD1):c.1274G>A (p.Arg425His) AND not provided | ClinVar | Detail |
| NM_000036.3(AMPD1):c.1274G>A (p.Arg425His) AND not specified | 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
- rs121912682 dbSNP
- Genome
- hg19
- Position
- chr1:115,220,086-115,220,086
- Variant Type
- snv
- Reference Allele
- C
- Alternative Allele
- T
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1206
- Mean of sample read depth (HGVD)
- 52.36
- Standard deviation of sample read depth (HGVD)
- 23.51
- Number of reference allele (HGVD)
- 2402
- Number of alternative allele (HGVD)
- 10
- Allele Frequency (HGVD)
- 0.0041459369817578775
- Gene Symbol (HGVD)
- AMPD1
- 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))
- rs121912682
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0035
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 59
- 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)
- 92
- East Asian Heterozygous Counts (ExAC)
- 92
- East Asian Homozygous Counts (ExAC)
- 0
- East Asian Allele Frequency (ExAC)
- 0.010630922116940143
- Chromosome Counts in All Race (ExAC)
- 121396
- Allele Counts in All Race (ExAC)
- 94
- Heterozygous Counts in All Race (ExAC)
- 94
- Homozygous Counts in All Race (ExAC)
- 0
- Allele Frequency in All Race (ExAC)
- 7.743253484464068E-4
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