VCV001711743.1 - ClinVar

NC_000008.11:g.129633446A>G

Germline

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.

(1)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

risk factor

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NC_000008.11:g.129633446A>G

Variation ID: 1711743 Accession: VCV001711743.1

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 8q24.21 8: 129633446 (GRCh38) [ NCBI UCSC ] 8: 130645692 (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	Oct 30, 2022	Oct 29, 2022	Oct 20, 2022

HGVS

Nucleotide	Protein	Molecular consequence
NC_000008.11:g.129633446A>G
NC_000008.10:g.130645692A>G
NG_053808.1:g.1703A>G

Protein change

Other names

Canonical SPDI

NC_000008.11:129633445:A:G

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

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.

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

Links

OMIM: 613040.0001 dbSNP: rs55705857 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.
CCDC26		-	-	GRCh38	-	23
LOC110121191	-	-	-	GRCh38	-	23

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.
Glioma susceptibility 7	risk factor (1)	no assertion criteria provided	Oct 20, 2022	RCV002293290.1

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.	More information 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.
risk factor (Oct 20, 2022)	no assertion criteria provided Method: literature only	GLIOMA SUSCEPTIBILITY 7 Affected status: not provided Allele origin: germline	OMIM Accession: SCV002586257.1 First in ClinVar: Oct 29, 2022 Last updated: Oct 29, 2022	Publications: PubMed (1) PubMed: 36201590 Comment on evidence: Yanchus et al. (2022) identified the G allele of the SNP rs55705857 as the causative risk variant for susceptibility to IDH1 (147700)/IDH2 (147650)-mutant low-grade glioma … (more) Yanchus et al. (2022) identified the G allele of the SNP rs55705857 as the causative risk variant for susceptibility to IDH1 (147700)/IDH2 (147650)-mutant low-grade glioma at the 8q24.21 locus (GLM7; 613032). The SNP rs55705857 is located in an intron of the long noncoding RNA CCDC26, within a brain- and melanocyte-specific enhancer that is active in selective cell lineages including embryonic precursor cells that give rise to adult neuronal stem cells (NSCs) and oligodendrocyte precursor cells (OPCs). Yanchus et al. (2022) showed that mechanistically, the rs55705857-G risk allele abrogates OCT2/4 (164176/164177) binding to this enhancer and exhibits increased physical interactions with the MYC (190080) promoter and increased MYC transcription, indicating that OCT2/4 binding of the nonrisk rs55705857-A allele restricts MYC expression. The nonrisk rs55705857-A allele and its surrounding sequence is completely conserved across all mammalian species through platypus. (less)

Germline Functional Evidence

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 germline classification of this variant

Title	Author	Journal	Year	Link
A noncoding single-nucleotide polymorphism at 8q24 drives IDH1-mutant glioma formation.	Yanchus C	Science (New York, N.Y.)	2022	PMID: 36201590

Text-mined citations for rs55705857 ...

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 Nov 05, 2022

ClinVar Genomic variation as it relates to human health

NC_000008.11:g.129633446A>G

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs55705857 ...