NM_000543.5(SMPD1):c.1763C>T (p.Thr588Met) AND not provided

Clinical significance:Benign/Likely benign (Last evaluated: Jun 13, 2018)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000224009.5

Allele description [Variation Report for NM_000543.5(SMPD1):c.1763C>T (p.Thr588Met)]

NM_000543.5(SMPD1):c.1763C>T (p.Thr588Met)

Gene:
SMPD1:sphingomyelin phosphodiesterase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11p15.4
Genomic location:
Preferred name:
NM_000543.5(SMPD1):c.1763C>T (p.Thr588Met)
HGVS:
  • NC_000011.10:g.6394474C>T
  • NG_011780.1:g.9050C>T
  • NG_029615.1:g.29941G>A
  • NM_000543.5:c.1763C>TMANE SELECT
  • NM_001007593.3:c.1760C>T
  • NM_001318087.2:c.*256C>T
  • NM_001318088.2:c.842C>T
  • NM_001365135.2:c.1631C>T
  • NP_000534.3:p.Thr588Met
  • NP_001007594.2:p.Thr587Met
  • NP_001305017.1:p.Thr281Met
  • NP_001352064.1:p.Thr544Met
  • NC_000011.9:g.6415704C>T
  • NM_000543.4:c.1763C>T
  • NR_027400.3:n.1716C>T
  • NR_134502.2:n.1255C>T
Protein change:
T281M
Links:
dbSNP: rs35785620
NCBI 1000 Genomes Browser:
rs35785620
Molecular consequence:
  • NM_001318087.2:c.*256C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_000543.5:c.1763C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001007593.3:c.1760C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001318088.2:c.842C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001365135.2:c.1631C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_027400.3:n.1716C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_134502.2:n.1255C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000280711Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinicscriteria provided, single submitter
Likely Benign
(Aug 25, 2015)
germlineclinical testing

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

SCV000986309GeneDxcriteria provided, single submitter
Benign
(Jun 13, 2018)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics, SCV000280711.1

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

Description

Converted during submission to Likely benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot provided0.003251not providednot provided

From GeneDx, SCV000986309.1

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

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

Last Updated: Nov 27, 2021

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