VCV001169347.14 - ClinVar

NM_014314.4(RIGI):c.2400A>C (p.Val800=)

Germline

Classification

criteria provided, multiple submitters, no conflicts. Learn more about how ClinVar calculates review status.

Benign
Benign (4)

4 out of 4 submissions contributed to this classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value 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

Identifiers

NM_014314.4(RIGI):c.2400A>C (p.Val800=)

Variation ID: 1169347 Accession: VCV001169347.14

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 9p21.1 9: 32459452 (GRCh38) [ NCBI UCSC ] 9: 32459450 (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	Jun 15, 2021	Feb 23, 2026	Feb 4, 2026

HGVS

Nucleotide	Protein	Molecular consequence
NM_014314.4:c.2400A>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_055129.2:p.Val800=	synonymous
NM_001385907.1:c.2394A>C	NP_001372836.1:p.Val798=	synonymous
NM_001385909.1:c.2229A>C	NP_001372838.1:p.Val743=	synonymous
NM_001385910.1:c.1959A>C	NP_001372839.1:p.Val653=	synonymous
NM_001385912.1:c.1791A>C	NP_001372841.1:p.Val597=	synonymous
NM_001385913.1:c.2385A>C	NP_001372842.1:p.Val795=	synonymous
NM_001385914.1:c.1956A>C	NP_001372843.1:p.Val652=	synonymous
NC_000009.12:g.32459452T>G
NC_000009.11:g.32459450T>G
NG_046918.1:g.71873A>C

... more HGVS ... less HGVS

Protein change

Other names

p.Val800=

Canonical SPDI

NC_000009.12:32459451:T:G

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.

0.31430 (G)

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

The Genome Aggregation Database (gnomAD), exomes 0.34612

NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.32108

Exome Aggregation Consortium (ExAC) 0.34605

1000 Genomes Project 0.31430

Trans-Omics for Precision Medicine (TOPMed) 0.32699

1000 Genomes Project 30x 0.31246

The Genome Aggregation Database (gnomAD), exomes 0.34933

Links

ClinGen: CA5019503 dbSNP: rs3205166 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.
LOC101060445	-	-	-	GRCh38	-	80
RIGI		-	-	GRCh38 GRCh37	736	881

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 (1)	criteria provided, single submitter	Feb 4, 2026	RCV001520480.9
Singleton-Merten syndrome 2	Benign (1)	criteria provided, single submitter	Jul 30, 2021	RCV001658221.3
not specified	Benign (2)	criteria provided, multiple submitters, no conflicts	Nov 14, 2023	RCV003399306.4

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.
Benign (Jul 30, 2021) C Contributing to aggregate classification	criteria provided, single submitter (ACMG Guidelines, 2015)	Singleton-Merten syndrome 2	Genome-Nilou Lab Accession: SCV001876621.2 First in ClinVar: Sep 19, 2021 Last updated: Apr 13, 2025	Observation: 1 Collection method: clinical testing Allele origin: germline Affected status: no more Observation 1 Collection method: clinical testing Allele origin: germline Affected status: no Sex: mixed

Benign (Nov 14, 2023) C Contributing to aggregate classification	criteria provided, single submitter (ACMG Guidelines, 2015)	not specified	Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan Accession: SCV004122993.2 First in ClinVar: Nov 20, 2023 Last updated: Apr 13, 2025	Publications: PubMed (1) PubMed: 25741868 Comment: show This variant is classified as Benign based on local population frequency. This variant was detected in 52% of patients studied by a panel of primary immunodeficiencies. Number of patients: 50. Only high quality variants are reported. (less) Observation: 1 Collection method: clinical testing Allele origin: germline Affected status: no more Observation 1 Collection method: clinical testing Allele origin: germline Affected status: no Number of individuals with the variant: 50 Age: <18 years Sex: mixed

Benign (Sep 06, 2022) C Contributing to aggregate classification	criteria provided, single submitter (ACMG Guidelines, 2015)	Not specified	Mayo Clinic Laboratories, Mayo Clinic Accession: SCV007301162.1 First in ClinVar: Jan 17, 2026 Last updated: Jan 17, 2026	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: 246

Benign (Feb 04, 2026) C Contributing to aggregate classification	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	not provided	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV001729588.6 First in ClinVar: Jun 15, 2021 Last updated: Feb 23, 2026	Observation: 1 Collection method: clinical testing Allele origin: germline Affected status: unknown Observation 1 Collection method: clinical testing Allele origin: germline Affected status: unknown

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.	Richards S	Genetics in medicine : official journal of the American College of Medical Genetics	2015	PMID: 25741868

Text-mined citations for rs3205166 ...

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 Mar 01, 2026