VCV000039357.69 - ClinVar

NM_000769.1(CYP2C19):c.-806C>T

Germline

Practice guidelines

Practice guidelines. Learn more about how ClinVar calculates review status.

Drug response

for CYP2C19: increased function

Classification is based on the practice guideline submission

by Clinical Pharmacogenetics Implementation Consortium

The classification is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

This variant is part of 67 Genotypes

This variant is part of a Haplotype

CYP2C19*4B

Identifiers

NM_000769.1(CYP2C19):c.-806C>T

Variation ID: 39357 Accession: VCV000039357.69

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 10q23.33 10: 94761900 (GRCh38) [ NCBI UCSC ] 10: 96521657 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Dec 6, 2016	Aug 3, 2025

HGVS

Nucleotide	Protein	Molecular consequence
NM_000769.4:c.-806C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NC_000010.11:g.94761900C>T
NC_000010.10:g.96521657C>T
NG_008384.3:g.4220C>T
NG_055436.1:g.1260C>T

... more HGVS ... less HGVS

Protein change

Other names

CYP2C19*17

Canonical SPDI

NC_000010.11:94761899:C:T

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

0.15315 (T)

Allele frequency Help The frequency of the allele represented by this VCV record.

1000 Genomes Project 0.15315

1000 Genomes Project 30x 0.15928

Trans-Omics for Precision Medicine (TOPMed) 0.19604

The Genome Aggregation Database (gnomAD) 0.19962

The Genome Aggregation Database (gnomAD) 0.20441

Links

ClinGen: CA10602359 Genetic Testing Registry (GTR): GTR000501203 Genetic Testing Registry (GTR): GTR000569929 Genetic Testing Registry (GTR): GTR000613302 dbSNP: rs12248560 VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
CYP2C19		-	-	GRCh38 GRCh37	266	701
LOC110599570	-	-	-	GRCh38	-	178

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
not provided	Benign; other (2)	criteria provided, multiple submitters, no conflicts	Mar 14, 2018	RCV000326411.16
CYP2C19: increased function	drug response (1)	practice guideline	-	RCV000782438.11
Clopidogrel response	drug response (1)	no assertion criteria provided	-	RCV004813048.2

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	Expand all rows Collapse all rows Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
drug response Allele function (-) C Contributing to aggregate classification	practice guideline (Clinical Pharmacogenetics Implementation Consortium)	CYP2C19: increased function	Clinical Pharmacogenetics Implementation Consortium Accession: SCV000920961.2 First in ClinVar: Jun 17, 2019 Last updated: Aug 03, 2025	Other databases https://www.pharmgkb.org/haploty… https://www.pharmgkb.org/haplotype/PA166128332 https://cpicpgx.org https://cpicpgx.org Observation: 1 Collection method: curation Allele origin: germline Affected status: not applicable more Observation 1 Collection method: curation Allele origin: germline Affected status: not applicable Comment on evidence: "Increased function" was previously submitted as the functional consequence for CYP2C19*17, but without providing the result of a functional assay.

Benign (Mar 14, 2018) N Not contributing to aggregate classification	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Not Provided	GeneDx Accession: SCV000976958.1 First in ClinVar: Aug 26, 2019 Last updated: Aug 26, 2019	Comment: show 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) Observation: 1 Collection method: clinical testing Allele origin: germline Affected status: yes Observation 1 Collection method: clinical testing Allele origin: germline Affected status: yes

other Variant classified as "other reportable" ??? variant is clinically benign (not associated with disease) but is reported when observed (e.g. pseudodeficiency alleles). (Jul 09, 2015) N Not contributing to aggregate classification	criteria provided, single submitter (EGL Classification Definitions 2015)	not provided	Eurofins Ntd Llc (ga) Accession: SCV000331711.4 First in ClinVar: Dec 06, 2016 Last updated: Apr 13, 2025	Other databases http://www.egl-eurofins.com/emvc… http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=CYP2C19 Observation: 1 Collection method: clinical testing Allele origin: germline Affected status: unknown more Observation 1 Collection method: clinical testing Allele origin: germline Affected status: unknown Number of individuals with the variant: 316 Zygosity: Homozygote, Single Heterozygote Sex: mixed

drug response over responsive (-) N Not contributing to aggregate classification	no assertion criteria provided	Clopidogrel Response Drug used for Coronary Artery Disease	Faculty of Pharmacy, Damascus University Accession: SCV005438653.2 First in ClinVar: Dec 22, 2024 Last updated: Apr 13, 2025	Comment: show rs12248560 is a SNP in the CYP2C19 gene and is linked to increased clopidogrel metabolic activation. rs12248560 is associated with increased enzyme activity of CYP2C19 and higher concentration of clopidogrel active metabolite. (less) Observation: 1 Collection method: research Allele origin: germline Affected status: yes more Observation 1 Collection method: research Allele origin: germline Affected status: yes Sex: mixed Geographic origin: Syria

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 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.

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=CYP2C19	-	-	-	-
https://www.pharmgkb.org/haplotype/PA166128332	-	-	-	-
https://cpicpgx.org	-	-	-	-

Text-mined citations for rs12248560 ...

These 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 Jan 11, 2026