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NM_000543.5(SMPD1):c.1071C>T (p.Ala357=) AND Niemann-Pick disease, type A

Germline classification:
Benign/Likely benign (3 submissions)
Last evaluated:
May 18, 2021
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000394529.10

Allele description [Variation Report for NM_000543.5(SMPD1):c.1071C>T (p.Ala357=)]

NM_000543.5(SMPD1):c.1071C>T (p.Ala357=)

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.1071C>T (p.Ala357=)
HGVS:
  • NC_000011.10:g.6392136C>T
  • NG_011780.1:g.6712C>T
  • NM_000543.5:c.1071C>TMANE SELECT
  • NM_001007593.3:c.1068C>T
  • NM_001318087.2:c.1071C>T
  • NM_001318088.2:c.110C>T
  • NM_001365135.2:c.1071C>T
  • NP_000534.3:p.Ala357=
  • NP_001007594.2:p.Ala356=
  • NP_001305016.1:p.Ala357=
  • NP_001305017.1:p.Pro37Leu
  • NP_001352064.1:p.Ala357=
  • NC_000011.9:g.6413366C>T
  • NM_000543.4(SMPD1):c.1071C>T
  • NM_000543.4:c.1071C>T
  • NP_000534.3:p.(=)
  • NR_027400.3:n.1196C>T
  • p.Ala357=
Protein change:
P37L
Links:
dbSNP: rs72896268
NCBI 1000 Genomes Browser:
rs72896268
Molecular consequence:
  • NM_001318088.2:c.110C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_027400.3:n.1196C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_000543.5:c.1071C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001007593.3:c.1068C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001318087.2:c.1071C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001365135.2:c.1071C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Niemann-Pick disease, type A
Synonyms:
SPHINGOMYELIN LIPIDOSIS; SPHINGOMYELINASE DEFICIENCY
Identifiers:
MONDO: MONDO:0009756; MedGen: C0268242; Orphanet: 77292; OMIM: 257200

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000372937Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)		Likely benign
(Jan 12, 2018) 		germlineclinical testing

Citation Link,

SCV001716378Genome-Nilou Lab
criteria provided, single submitter

(ACMG Guidelines, 2015)		Benign
(May 18, 2021) 		germlineclinical testing

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

SCV002092260Natera, Inc.
no assertion criteria provided
Benign
(Mar 29, 2017) 		germlineclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenonot 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 Illumina Laboratory Services, Illumina, SCV000372937.3

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

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.

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

From Genome-Nilou Lab, SCV001716378.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenonot providednot providednot providednot providednot providednot providednot provided

From Natera, Inc., SCV002092260.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 20, 2024