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NM_207122.2(EXT2):c.626+3A>C AND Multiple congenital exostosis

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 24, 2021
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV001543120.2

Allele description [Variation Report for NM_207122.2(EXT2):c.626+3A>C]

NM_207122.2(EXT2):c.626+3A>C

Gene:
EXT2:exostosin glycosyltransferase 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11p11.2
Genomic location:
Preferred name:
NM_207122.2(EXT2):c.626+3A>C
HGVS:
  • NC_000011.10:g.44109286A>C
  • NG_007560.1:g.18738A>C
  • NM_000401.3:c.725+3A>C
  • NM_001178083.3:c.626+3A>C
  • NM_207122.2:c.626+3A>CMANE SELECT
  • LRG_494t1:c.725+3A>C
  • LRG_494:g.18738A>C
  • NC_000011.9:g.44130836A>C
Links:
dbSNP: rs200934340
NCBI 1000 Genomes Browser:
rs200934340
Molecular consequence:
  • NM_000401.3:c.725+3A>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001178083.3:c.626+3A>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_207122.2:c.626+3A>C - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Multiple congenital exostosis (EXT)
Synonyms:
MULTIPLE CARTILAGINOUS EXOSTOSES; Hereditary multiple osteochondromas; Multiple exostoses; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0005508; MedGen: C0015306; Orphanet: 321; OMIM: PS133700; Human Phenotype Ontology: HP:0002762

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001761637St. Jude Molecular Pathology, St. Jude Children's Research Hospital
criteria provided, single submitter

(St. Jude Assertion Criteria 2020)		Uncertain significance
(Jun 24, 2021) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From St. Jude Molecular Pathology, St. Jude Children's Research Hospital, SCV001761637.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The EXT2 c.725+3A>C intronic change results from a A to C substitution at the +3 position of intron 4 of the EXT2 gene. Splice predictors are not conclusive as to whether or not this variant affects splicing and loss of function of the resulting protein product. RNA data demonstrates aberrant splicing in ~6-7% of mutant reads (internal data). This variant has a maximum subpopulation frequency of 0.0023% in gnomAD v2.1.1 (PM2_Supporting; https://gnomad.broadinstitute.org/variant/11-44130836-A-C?dataset=gnomad_r2_1). In summary, this variant meets criteria to be classified as of uncertain significance based on the ACMG/AMP criteria: PM2_Supporting.

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

Last Updated: Mar 30, 2024