NM_012431.3(SEMA3E):c.116-10T>A AND CHARGE association

Clinical significance:Uncertain significance (Last evaluated: Mar 19, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000706063.3

Allele description [Variation Report for NM_012431.3(SEMA3E):c.116-10T>A]

NM_012431.3(SEMA3E):c.116-10T>A

Gene:
SEMA3E:semaphorin 3E [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7q21.11
Genomic location:
Preferred name:
NM_012431.3(SEMA3E):c.116-10T>A
HGVS:
  • NC_000007.14:g.83490284A>T
  • NG_021242.2:g.163880T>A
  • NM_001178129.2:c.-65-10T>A
  • NM_012431.3:c.116-10T>AMANE SELECT
  • LRG_1287t1:c.116-10T>A
  • LRG_1287:g.163880T>A
  • NC_000007.13:g.83119600A>T
  • NM_012431.2:c.116-10T>A
Links:
dbSNP: rs1562804630
NCBI 1000 Genomes Browser:
rs1562804630
Molecular consequence:
  • NM_001178129.2:c.-65-10T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_012431.3:c.116-10T>A - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
CHARGE association (CHARGE)
Synonyms:
CHARGE ASSOCIATION--COLOBOMA, HEART ANOMALY, CHOANAL ATRESIA, RETARDATION, GENITAL AND EAR ANOMALIES; CHARGE syndrome; Coloboma, heart anomaly, choanal atresia, retardation, genital and ear anomalies; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0008965; MedGen: C0265354; Orphanet: 138; OMIM: 214800

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000835093Invitaecriteria provided, single submitter
Uncertain significance
(Mar 19, 2019)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000835093.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This sequence change falls in intron 1 of the SEMA3E gene. It does not directly change the encoded amino acid sequence of the SEMA3E protein. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with SEMA3E-related disease. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Oct 30, 2021

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