VCV000140587.4 - ClinVar

NC_012920.1(MT-CYB):m.14766C>T

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.

(3)

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.

Benign

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NC_012920.1(MT-CYB):m.14766C>T

Variation ID: 140587 Accession: VCV000140587.4

Type and length

single nucleotide variant, 1 bp

Location

MT: 14766 (GRCh38) [ NCBI UCSC ] MT: 14766 (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	Jul 25, 2014	Mar 10, 2024	Oct 17, 2019

HGVS

Nucleotide	Protein	Molecular consequence
NC_012920.1:m.14766C>T

Protein change

Other names

Canonical SPDI

NC_012920.1:14765:C:T

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

dbSNP: rs193302980 ClinGen: CA345703 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.
MT-CYB		-	-	GRCh38	321	328

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.
Familial cancer of breast	Likely pathogenic (1)	no assertion criteria provided	-	RCV000128802.3
Leigh syndrome	Benign (1)	criteria provided, single submitter	Oct 17, 2019	RCV000855150.2
Venous thromboembolism	Likely risk allele (1)	no assertion criteria provided	-	RCV003886377.1

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.
Benign (Oct 17, 2019)	criteria provided, single submitter (Modified ACMG Guidelines (Unpublished)) Method: clinical testing	Leigh syndrome Affected status: unknown Allele origin: germline	Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine Accession: SCV000998200.1 First in ClinVar: Nov 02, 2019 Last updated: Nov 02, 2019	Comment: The NC_012920.1:m.14766C>T (YP_003024038.1:p.Thr7Ile) variant in MTCYB gene is interpretated to be a Benign variant based on the modified ACMG guidelines (unpublished). This variant meets the … (more) The NC_012920.1:m.14766C>T (YP_003024038.1:p.Thr7Ile) variant in MTCYB gene is interpretated to be a Benign variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes: BA1 (less)
probable-pathogenic (-)	no assertion criteria provided Method: not provided	Familial cancer of breast Affected status: not provided Allele origin: unknown	Department of Zoology Govt. MVM College Accession: SCV000172460.1 First in ClinVar: Jul 25, 2014 Last updated: Jul 25, 2014 Comment: Our Seq: KM077020	Comment: Converted during submission to Likely pathogenic.
Likely risk allele (-)	no assertion criteria provided Method: case-control	VENOUS THROMBOEMBOLISM (Mitochondrial inheritance) Affected status: yes Allele origin: maternal	Genomics Division, Defence Institute of Physiology and Allied Sciences Accession: SCV004698205.1 First in ClinVar: Mar 10, 2024 Last updated: Mar 10, 2024	Number of individuals with the variant: 11 Age: 29-43 years Sex: male Ethnicity/Population group: Asian Geographic origin: India Comment on evidence: Three age and sex matched study groups were taken and whole exome sequencing was performed. 1. Healthy Subjects (n=19) 2. Sea Level Venous Thromboembolism (n=15) … (more) Three age and sex matched study groups were taken and whole exome sequencing was performed. 1. Healthy Subjects (n=19) 2. Sea Level Venous Thromboembolism (n=15) 3. High Altitude Venous Thromboembolism (n=6) After analysis we found frequency of rs193302980 in sea level as well as high altitude induced Thromboembolism study groups. However, this SNP was absent in Healthy Subjects. First time it is being reporting association of rs193302980 with Venous Thromboembolism. (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

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 rs193302980 ...

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 Sep 08, 2024

ClinVar Genomic variation as it relates to human health

NC_012920.1(MT-CYB):m.14766C>T

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs193302980 ...