VCV000984916.1 - ClinVar

NC_000004.12:g.1113690T>C

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_000004.12:g.1113690T>C

Variation ID: 984916 Accession: VCV000984916.1

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 4p16.3 4: 1113690 (GRCh38) [ NCBI UCSC ] 4: 1107478 (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	Nov 21, 2020	Nov 21, 2020	Sep 10, 2019

HGVS

Nucleotide	Protein	Molecular consequence
NR_134676.1:n.52T>C		non-coding transcript variant
NC_000004.12:g.1113690T>C
NC_000004.11:g.1107478T>C
NG_027812.2:g.5105A>G

Protein change

Other names

Canonical SPDI

NC_000004.12:1113689:T:C

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

Uncertain function

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.

0.41134 (T)

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

1000 Genomes Project 30x 0.58182

The Genome Aggregation Database (gnomAD) 0.61416

1000 Genomes Project 0.58866

Trans-Omics for Precision Medicine (TOPMed) 0.60654

Links

dbSNP: rs62296477 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.
LOC105374344	-	-	-	GRCh38	-	72
RNF212		-	-	GRCh38 GRCh37	35	184

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.
Down syndrome	risk factor (1)	no assertion criteria provided	Sep 10, 2019	RCV001265538.1

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 (Sep 10, 2019)	no assertion criteria provided Method: case-control	Down syndrome Affected status: yes Allele origin: maternal	Cytogenetics & Genomics Research Unit, University of Calcutta Accession: SCV001441567.1 First in ClinVar: Nov 21, 2020 Last updated: Nov 21, 2020	Comment: This was a variant found in the promoter region of RNF212 from mothers that has down syndrome child. We anticipate this variant as a significant … (more) This was a variant found in the promoter region of RNF212 from mothers that has down syndrome child. We anticipate this variant as a significant risk factor. (less) Number of individuals with the variant: 680 Zygosity: Homozygote, Single Heterozygote, Compound Heterozygote, Hemizygote Age: 18-40 years Sex: female Ethnicity/Population group: Bengali Geographic origin: India Comment on evidence: Around 680 maternal RNF212 gene were screened for polymorphisms by Sanger DNA sequencing. We found the above mentioned variant within the promoter region of the … (more) Around 680 maternal RNF212 gene were screened for polymorphisms by Sanger DNA sequencing. We found the above mentioned variant within the promoter region of the gene and it was found to be associated as a risk factor for Down Syndrome Child birth. (less)

Germline Functional Evidence

Functional Help The functional consequence of the variant, based on experimental evidence and provided by the submitter. consequence	Method Help A brief description of the method used to determine the functional consequence of the variant. A citation for the method is included, when provided by the submitter.	Result Help A brief description of the result of this method for 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 functional evidence for the germline classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Uncertain function			Cytogenetics & Genomics Research Unit, University of Calcutta Accession: SCV001441567.1

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs62296477 ...

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 Oct 08, 2024

ClinVar Genomic variation as it relates to human health

NC_000004.12:g.1113690T>C

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs62296477 ...