chr12:40646786:C>T Detail (hg19) (LRRK2)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr12:40,646,786-40,646,786 |
| hg38 | chr12:40,252,984-40,252,984 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_198578.3:c.1256C>T | NP_940980.3:p.Ala419Val |
| Ensemble | ENST00000298910.12:c.1256C>T | ENST00000298910.12:p.Ala419Val |
| ENST00000343742.6:c.1256C>T | ENST00000343742.6:p.Ala419Val |
Summary
MGeND
| Clinical significance |
Benign
|
| Variant entry | 1 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.020 |
| ToMMo:0.015 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.006 |
Prediction
ClinVar
| Clinical Significance |
Benign
Likely benign
|
| 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 |
|---|---|---|---|---|---|
|
Benign
Likely benign
|
2023-11-15 | criteria provided, multiple submitters, no conflicts | Autosomal dominant Parkinson disease 8 |
germline
unknown
|
Detail |
|
Benign
Likely benign
|
2023-08-01 | criteria provided, multiple submitters, no conflicts | not provided |
germline
|
Detail |
|
Likely benign
|
2024-01-25 | criteria provided, single submitter | LRRK2-related disorder |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.440 | PARKINSON DISEASE 8 (disorder) | NA | CLINVAR | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_198578.4(LRRK2):c.1256C>T (p.Ala419Val) AND Autosomal dominant Parkinson disease 8 | ClinVar | Detail |
| NM_198578.4(LRRK2):c.1256C>T (p.Ala419Val) AND not provided | ClinVar | Detail |
| NM_198578.4(LRRK2):c.1256C>T (p.Ala419Val) AND LRRK2-related disorder | 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
- rs34594498 dbSNP
- Genome
- hg19
- Position
- chr12:40,646,786-40,646,786
- Variant Type
- snv
- Reference Allele
- C
- Alternative Allele
- T
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1209
- Mean of sample read depth (HGVD)
- 68.75
- Standard deviation of sample read depth (HGVD)
- 28.96
- Number of reference allele (HGVD)
- 2370
- Number of alternative allele (HGVD)
- 48
- Allele Frequency (HGVD)
- 0.019851116625310174
- Gene Symbol (HGVD)
- LRRK2
- 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))
- rs34594498
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0154
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 258
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8626
- East Asian Allele Counts (ExAC)
- 50
- East Asian Heterozygous Counts (ExAC)
- 50
- East Asian Homozygous Counts (ExAC)
- 0
- East Asian Allele Frequency (ExAC)
- 0.005796429399489914
- Chromosome Counts in All Race (ExAC)
- 120628
- Allele Counts in All Race (ExAC)
- 62
- Heterozygous Counts in All Race (ExAC)
- 62
- Homozygous Counts in All Race (ExAC)
- 0
- Allele Frequency in All Race (ExAC)
- 5.139768544616507E-4
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