VCV000042206.5 - ClinVar

NC_012920.1(MT-CYB):m.1193T>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.

(2)

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/Likely benign

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NC_012920.1(MT-CYB):m.1193T>C

Variation ID: 42206 Accession: VCV000042206.5

Type and length

single nucleotide variant, 1 bp

Location

MT: 1193 (GRCh38) [ NCBI UCSC ] MT: 1193 (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	Apr 9, 2018	Jan 19, 2020	Dec 12, 2018

HGVS

Nucleotide	Protein	Molecular consequence
NC_012920.1:m.1193T>C

Protein change

Other names

Canonical SPDI

NC_012920.1:1192:T:C

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

ClinGen: CA130993 dbSNP: rs111033321 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-RNR1		-	-	GRCh38	76	80

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 specified	Likely benign (1)	criteria provided, single submitter	Feb 18, 2014	RCV000035030.6
not provided	Benign (1)	criteria provided, single submitter	Dec 12, 2018	RCV000992376.2

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 benign (Feb 18, 2014)	criteria provided, single submitter (LMM Criteria) Method: clinical testing	not specified Affected status: not provided Allele origin: germline	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine Accession: SCV000058670.5 First in ClinVar: May 03, 2013 Last updated: Apr 09, 2018	Publications: PubMed (1) PubMed: 23969527 Comment: m.1193T>C in MTRNR1: This variant is not expected to have clinical significance because it has been identified at frequencies ranging from 0.2% to 33% across … (more) m.1193T>C in MTRNR1: This variant is not expected to have clinical significance because it has been identified at frequencies ranging from 0.2% to 33% across di fferent populations by phylogenetic studies (http://mitomap.org/MITOMAP, http:// www.mtdb.igp.uu.se). It has also been reported in 1/169 (0.59%) patients with he aring impairment (Guaran 2013). In summary, in the absence of any statistically significant association to hearing loss, the frequency of this variant suggests that it is likely benign. (less) Number of individuals with the variant: 5
Benign (Dec 12, 2018)	criteria provided, single submitter (Athena Diagnostics Criteria) Method: clinical testing	not provided Affected status: unknown Allele origin: germline	Athena Diagnostics Accession: SCV001144604.1 First in ClinVar: Jan 19, 2020 Last updated: Jan 19, 2020	Publications: PubMed (2) PubMed: 19371214‚ 23969527

Comment:

m.1193T>C in MTRNR1: This variant is not expected to have clinical significance because it has been identified at frequencies ranging from 0.2% to 33% across di fferent populations by phylogenetic studies (http://mitomap.org/MITOMAP, http:// www.mtdb.igp.uu.se). It has also been reported in 1/169 (0.59%) patients with he aring impairment (Guaran 2013). In summary, in the absence of any statistically significant association to hearing loss, the frequency of this variant suggests that it is likely benign.

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.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Association between idiopathic hearing loss and mitochondrial DNA mutations: a study on 169 hearing-impaired subjects.	Guaran V	International journal of molecular medicine	2013	PMID: 23969527
Screening of the general Polish population for deafness-associated mutations in mitochondrial 12S rRNA and tRNA Ser(UCN) genes.	Rydzanicz M	Genetic testing and molecular biomarkers	2009	PMID: 19371214

Text-mined citations for rs111033321 ...

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 May 08, 2024

ClinVar Genomic variation as it relates to human health

NC_012920.1(MT-CYB):m.1193T>C

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs111033321 ...