VCV000370060.2 - ClinVar

NC_012920.1:m.14706A>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.

(4)

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:m.14706A>G

Variation ID: 370060 Accession: VCV000370060.2

Type and length

single nucleotide variant, 1 bp

Location

MT: 14706 (GRCh38) [ NCBI UCSC ] MT: 14706 (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	Jan 4, 2017	Sep 22, 2019	Jul 12, 2019

HGVS

Nucleotide	Protein	Molecular consequence
NC_012920.1:m.14706A>G

Protein change

Other names

Canonical SPDI

NC_012920.1:14705: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

ClinGen: CA16040637 dbSNP: rs1057516070 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-TE		-	-	GRCh38	23	30

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.
Episodic vomiting Mild liver congestion Sudden death	Uncertain significance (1)	no assertion criteria provided	Nov 21, 2016	RCV000408927.1
Developmental delay	Uncertain significance (1)	no assertion criteria provided	Nov 21, 2016	RCV000408954.1
not provided	not provided (1)	no classification provided	-	RCV000662335.1
Juvenile myopathy, encephalopathy, lactic acidosis AND stroke	Benign (1)	criteria provided, single submitter	Jul 12, 2019	RCV000851097.1

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 (Jul 12, 2019)	criteria provided, single submitter (Modified ACMG Guidelines (Unpublished)) Method: clinical testing	Juvenile myopathy, encephalopathy, lactic acidosis AND stroke Affected status: unknown Allele origin: germline	Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine Accession: SCV000993331.1 First in ClinVar: Sep 22, 2019 Last updated: Sep 22, 2019	Publications: PubMed (1) PubMed: 31965079 Comment: The NC_012920.1:m.14706A>G variant in MT-TE gene is interpreted to be a Benign variant based on the modified ACMG guidelines (unpublished). This variant meets the following … (more) The NC_012920.1:m.14706A>G variant in MT-TE gene is interpreted to be a Benign variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes reported in the guidelines: BS1, BS4, BP4 (less)
Uncertain significance (Nov 21, 2016)	no assertion criteria provided Method: clinical testing	Developmental delay Affected status: yes Allele origin: unknown	Center for Neuroscience and Cell Biology, University of Coimbra, Portugal Accession: SCV000484536.1 First in ClinVar: Jan 04, 2017 Last updated: Jan 04, 2017	Publications: PubMed (1) PubMed: 28027978 Number of individuals with the variant: 2 Sex: female Ethnicity/Population group: Caucasian
Uncertain significance (Nov 21, 2016)	no assertion criteria provided Method: clinical testing	Frequent vomiting Mild liver congestion Sudden death Affected status: yes Allele origin: unknown	Center for Neuroscience and Cell Biology, University of Coimbra, Portugal Accession: SCV000484537.1 First in ClinVar: Jan 04, 2017 Last updated: Jan 04, 2017	Publications: PubMed (1) PubMed: 28027978 Number of individuals with the variant: 2 Sex: male Ethnicity/Population group: Caucasian
not provided (-)	no classification provided Method: phenotyping only	Not Provided Affected status: unknown Allele origin: unknown	GenomeConnect, ClinGen Accession: SCV000784693.1 First in ClinVar: Jul 16, 2018 Last updated: Jul 16, 2018	Comment: GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical … (more) GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. (less) Clinical Features: Short stature (present) , Delayed puberty (present) , Hypermetropia (present) , Vertigo (present) , Hyperacusis (present) , Tinnitus (present) , Memory impairment (present) , Depressivity … (more) Short stature (present) , Delayed puberty (present) , Hypermetropia (present) , Vertigo (present) , Hyperacusis (present) , Tinnitus (present) , Memory impairment (present) , Depressivity (present) , Anxiety (present) , Stereotypy (present) , Autistic behavior (present) , Joint hypermobility (present) , Asthma (present) , Abnormality of the intestine (present) , Abnormality of the liver (present) , Recurrent infections (present) , Abnormal inflammatory response (present) , Immunodeficiency (present) (less) Age: 40-49 years Sex: female Testing laboratory: GeneDx Date variant was reported to submitter: 2017-04-07 Testing laboratory interpretation: Uncertain significance

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
Interpretation of mitochondrial tRNA variants.	Wong LC	Genetics in medicine : official journal of the American College of Medical Genetics	2020	PMID: 31965079
In silico analysis for predicting pathogenicity of five unclassified mitochondrial DNA mutations associated with mitochondrial cytopathies' phenotypes.	Bacalhau M	European journal of medical genetics	2017	PMID: 28027978

Text-mined citations for rs1057516070 ...

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 Dec 11, 2022

ClinVar Genomic variation as it relates to human health

NC_012920.1:m.14706A>G

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs1057516070 ...