VCV000981242.2 - ClinVar

NC_000023.11:g.946718C>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.

Likely pathogenic

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NC_000023.11:g.946718C>G

Variation ID: 981242 Accession: VCV000981242.2

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: Xp22.33 Yp11.2 X: 946718 (GRCh38) [ NCBI UCSC ] Y: 946718 (GRCh38) [ NCBI UCSC ] X: 907453 (GRCh37) [ NCBI UCSC ] Y: 857453 (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 10, 2020	Oct 7, 2023	Jul 15, 2020

HGVS

Nucleotide	Protein	Molecular consequence
NC_000023.11:g.946718C>G
NC_000024.10:g.946718C>G
NC_000023.10:g.907453C>G
NC_000024.9:g.857453C>G

Protein change

Other names

CT78

Canonical SPDI

NC_000024.10:946717:C:G

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

variation affecting protein; Variation Ontology [ VariO:0002]

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

dbSNP: rs2088000353 VarSome

Genes

No affected genes found.

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.
Sudden infant death-dysgenesis of the testes syndrome	Likely pathogenic (1)	no assertion criteria provided	Jul 15, 2020	RCV001260590.1

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.
Likely pathogenic (Jul 15, 2020)	no assertion criteria provided Method: case-control	Sudden infant death-dysgenesis of the testes syndrome (Y-linked inheritance) Affected status: yes Allele origin: germline	Cytogenetics & Genomics Research Unit, University of Calcutta Accession: SCV001433667.2 First in ClinVar: Oct 10, 2020 Last updated: Oct 07, 2023	Comment: The novel transversion G>C in the Human TSPY1 gene is being reported for the first time in Bengali speaking population from India. This variant was … (more) The novel transversion G>C in the Human TSPY1 gene is being reported for the first time in Bengali speaking population from India. This variant was observed in males that are clinically infertile. Therefore, the cause of male infertility may be implicated by this variant. (less) Age: 25-56 years Sex: male Ethnicity/Population group: Bengali Geographic origin: India

Comment:

The novel transversion G>C in the Human TSPY1 gene is being reported for the first time in Bengali speaking population from India. This variant was observed in males that are clinically infertile. Therefore, the cause of male infertility may be implicated by this variant.

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.
variation affecting protein (VariO:0002)			Cytogenetics & Genomics Research Unit, University of Calcutta Accession: SCV001433667.2

Comment:

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 rs2088000353 ...

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 07, 2023

ClinVar Genomic variation as it relates to human health

NC_000023.11:g.946718C>G

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs2088000353 ...