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NM_004958.4(MTOR):c.3117+34G>A AND Overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes

Germline classification:
Benign (1 submission)
Last evaluated:
Feb 11, 2022
Review status:
3 stars out of maximum of 4 stars
reviewed by expert panel
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV001837022.10

Allele description [Variation Report for NM_004958.4(MTOR):c.3117+34G>A]

NM_004958.4(MTOR):c.3117+34G>A

Gene:
MTOR:mechanistic target of rapamycin kinase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p36.22
Genomic location:
Preferred name:
NM_004958.4(MTOR):c.3117+34G>A
Other names:
NM_004958.3:c.3117+34G>A
HGVS:
  • NC_000001.11:g.11216114C>T
  • NG_033239.1:g.51438G>A
  • NM_001386500.1:c.3117+34G>A
  • NM_001386501.1:c.1869+34G>A
  • NM_004958.4:c.3117+34G>AMANE SELECT
  • LRG_734:g.51438G>A
  • NC_000001.10:g.11276171C>T
Links:
dbSNP: rs545304092
NCBI 1000 Genomes Browser:
rs545304092
Molecular consequence:
  • NM_001386500.1:c.3117+34G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001386501.1:c.1869+34G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_004958.4:c.3117+34G>A - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes
Identifiers:
MONDO: MONDO:0100283; MedGen: CN300503

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001949978ClinGen Brain Malformations Variant Curation Expert Panel
reviewed by expert panel

(ClinGen BrainMalform ACMG Specifications v1)		Benign
(Feb 11, 2022) 		germlinecuration

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

Details of each submission

From ClinGen Brain Malformations Variant Curation Expert Panel, SCV001949978.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

This NM_004958.4(MTOR): c.3117+34G>A (p.=) variant is a synonymous (silent) variant that occurs at a nucleotide that is not conserved according to a PhyloP <0.1 (BP7). The results from in silico splicing predictors MaxEntScan, spliceAI and varSEAK support that this variant does not affect splicing (BP4). The highest population minor allele frequency in gnomAD v2.1.1 is 0.004847 in the South Asian population, which is higher than the ClinGen BMEP threshold ([>=0.00185]) for BA1, and therefore meets this criterion (BA1). This variant was identified the homozygous state in >3 individuals within control databases (BS2). In summary, this variant meets the criteria to be classified as Benign for mosaic autosomal dominant overgrowth with or without cerebral malformations due to abnormalities in MTOR-pathway genes based on the ACMG/AMP criteria applied, as specified by the ClinGen Brain Malformations Expert Panel: BA1, BP4, BP7, BS2 ; -14 points (VCEP specifications version 1; Approved: 1/31/2021)

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 24, 2024