chr2:219209648:C>T Detail (hg19) (PNKD, CATIP-AS2)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr2:219,209,648-219,209,648 |
| hg38 | chr2:218,344,925-218,344,925 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_015488.4:c.1102C>T | NP_056303.3:p.Arg368Trp |
| NM_022572.4:c.1030C>T | NP_072094.1:p.Arg344Trp | |
| Ensemble | ENST00000273077.9:c.1102C>T | ENST00000273077.9:p.Arg368Trp |
Summary
MGeND
| Clinical significance |
Benign
|
| Variant entry | 1 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.003 |
| ToMMo:0.003 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:<0.001 |
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 |
|---|---|---|---|---|---|
Likely benign
|
2024-01-17 | criteria provided, single submitter | Paroxysmal nonkinesigenic dyskinesia |
germline
|
Detail |
Uncertain significance
|
2023-02-02 | criteria provided, single submitter | paroxysmal nonkinesigenic dyskinesia 1 |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_015488.5(PNKD):c.1102C>T (p.Arg368Trp) AND Paroxysmal nonkinesigenic dyskinesia | ClinVar | Detail |
| NM_015488.5(PNKD):c.1102C>T (p.Arg368Trp) AND Paroxysmal nonkinesigenic dyskinesia 1 | 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
- rs185906233 dbSNP
- Genome
- hg19
- Position
- chr2:219,209,648-219,209,648
- Variant Type
- snv
- Reference Allele
- C
- Alternative Allele
- T
- Filtering Status (HGVD)
- PASS
- Filtering Status (HGVD)
- LowQual
- # of samples (HGVD)
- 1184
- Mean of sample read depth (HGVD)
- 21.30
- Standard deviation of sample read depth (HGVD)
- 20.06
- Number of reference allele (HGVD)
- 2361
- Number of alternative allele (HGVD)
- 7
- Allele Frequency (HGVD)
- 0.0029560810810810812
- Gene Symbol (HGVD)
- PNKD
- 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))
- rs185906233
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.003
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 51
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8616
- East Asian Allele Counts (ExAC)
- 7
- East Asian Heterozygous Counts (ExAC)
- 7
- East Asian Homozygous Counts (ExAC)
- 0
- East Asian Allele Frequency (ExAC)
- 8.124419684308263E-4
- Chromosome Counts in All Race (ExAC)
- 119372
- Allele Counts in All Race (ExAC)
- 7
- Heterozygous Counts in All Race (ExAC)
- 7
- Homozygous Counts in All Race (ExAC)
- 0
- Allele Frequency in All Race (ExAC)
- 5.864021713634688E-5
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