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NM_004863.4(SPTLC2):c.1470C>T (p.Asn490=) AND Inborn genetic diseases

Germline classification:
Likely benign (1 submission)
Last evaluated:
Jul 11, 2019
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:
RCV002388117.3

Allele description [Variation Report for NM_004863.4(SPTLC2):c.1470C>T (p.Asn490=)]

NM_004863.4(SPTLC2):c.1470C>T (p.Asn490=)

Gene:
SPTLC2:serine palmitoyltransferase long chain base subunit 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
14q24.3
Genomic location:
Preferred name:
NM_004863.4(SPTLC2):c.1470C>T (p.Asn490=)
HGVS:
  • NC_000014.9:g.77518137G>A
  • NG_028282.1:g.103631C>T
  • NM_004863.4:c.1470C>TMANE SELECT
  • NP_004854.1:p.Asn490=
  • NP_004854.1:p.Asn490=
  • LRG_371t1:c.1470C>T
  • LRG_371:g.103631C>T
  • LRG_371p1:p.Asn490=
  • NC_000014.8:g.77984480G>A
  • NM_004863.3:c.1470C>T
Links:
dbSNP: rs374657234
NCBI 1000 Genomes Browser:
rs374657234
Molecular consequence:
  • NM_004863.4:c.1470C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Inborn genetic diseases
Identifiers:
MeSH: D030342; MedGen: C0950123

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002702204Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely benign
(Jul 11, 2019) 		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 Ambry Genetics, SCV002702204.2

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

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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

Last Updated: Oct 20, 2024