This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
ClinVar Genomic variation as it relates to human health
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- Interpretation:
-
Benign; other
- Review status:
- criteria provided, multiple submitters, no conflicts
- Submissions:
- 2
- First in ClinVar:
- Apr 9, 2018
- Most recent Submission:
- Dec 16, 2018
- Last evaluated:
- Aug 6, 2018
- Accession:
- VCV000242701.4
- Variation ID:
- 242701
- Description:
- single nucleotide variant
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NM_000106.6(CYP2D6):c.1457G>C (p.Ser486Thr)
- Allele ID
- 38485
- Variant type
- single nucleotide variant
- Variant length
- 1 bp
- Cytogenetic location
- 22q13.2
- Genomic location
- 22: 42126611 (GRCh38) GRCh38 UCSC
- 22: 42522613 (GRCh37) GRCh37 UCSC
- HGVS
-
... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_000106.6:c.1457G>C MANE Select NP_000097.3:p.Ser486Thr missense NM_001025161.3:c.1304G>C NP_001020332.2:p.Ser435Thr missense NC_000022.11:g.42126611C>G NC_000022.10:g.42522613= NG_008376.3:g.8381G>C NG_008376.4:g.9200G>C LRG_303:g.9200G>C LRG_303t1:c.1457G>C LRG_303p1:p.Ser486Thr P10635:p.Ser486Thr - Protein change
- S486T, S435T
- Other names
- CYP2D6*17
- Canonical SPDI
- NC_000022.11:42126610:C:G
- Functional consequence
- Decreased function
- Global minor allele frequency (GMAF)
- -
- Allele frequency
- The Genome Aggregation Database (gnomAD) 0.57695
- Trans-Omics for Precision Medicine (TOPMed) 0.57811
- Links
- ClinGen: CA039095
- UniProtKB: P10635#VAR_008341
- OMIM: 124030.0007
- dbSNP: rs1135840
- VarSome
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Aggregate interpretations per condition
| Interpreted condition | Interpretation | Number of submissions | Review status | Last evaluated | Variation/condition record |
|---|---|---|---|---|---|
| Benign | 1 | criteria provided, single submitter | Feb 27, 2018 | RCV000609529.2 | |
| other | 1 | criteria provided, single submitter | Aug 6, 2018 | RCV000734610.4 |
Submitted interpretations and evidence
Help| Interpretation (Last evaluated) |
Review status (Assertion criteria) |
Condition (Inheritance) |
Submitter | More information | |
|---|---|---|---|---|---|
|
Benign
(Feb 27, 2018)
|
criteria provided, single submitter
Method: clinical testing
|
not specified
Affected status: yes
Allele origin:
germline
|
GeneDx
Accession: SCV000728215.1
First in ClinVar: Apr 09, 2018 Last updated: Apr 09, 2018 |
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. (less)
|
|
|
other
(Aug 06, 2018)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
germline
|
Eurofins NTD LLC (GA)
Accession: SCV000862764.1
First in ClinVar: Dec 16, 2018 Last updated: Dec 16, 2018 |
Sex: mixed
|
Functional evidence
Help| There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for this variant
Help| Title | Author | Journal | Year | Link |
|---|---|---|---|---|
| http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=CYP2D6 | - | - | - | - |
Text-mined citations for rs1135840...
HelpThese citations are identified by LitVar using
the rs number, so they may include citations for more than one variant
at this location. Please review the LitVar results carefully for your
variant of interest.
Record last updated Aug 16, 2022