NM_000543.5(SMPD1):c.108GCTGGC[5] (p.38AL[5]) AND not provided

Germline classification:: Benign (3 submissions)
Last evaluated:: Jul 5, 2018
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:: RCV000589078.7

Allele description [Variation Report for NM_000543.5(SMPD1):c.108GCTGGC[5] (p.38AL[5])]

NM_000543.5(SMPD1):c.108GCTGGC[5] (p.38AL[5])

Gene:

SMPD1:sphingomyelin phosphodiesterase 1 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

11p15.4

Genomic location:

Preferred name:

NM_000543.5(SMPD1):c.108GCTGGC[5] (p.38AL[5])

HGVS:

NC_000011.10:g.6390706GCTGGC[5]
NC_000011.9:g.6411936_6411941del
NG_011780.1:g.5282GCTGGC[5]
NM_000543.5:c.108GCTGGC[5]MANE SELECT
NM_001007593.3:c.108GCTGGC[5]
NM_001318087.2:c.108GCTGGC[5]
NM_001318088.2:c.-854GCTGGC[5]
NM_001365135.2:c.108GCTGGC[5]
NP_000534.3:p.38AL[5]
NP_001007594.2:p.38AL[5]
NP_001305016.1:p.38AL[5]
NP_001352064.1:p.38AL[5]
NC_000011.9:g.6411936GCTGGC[5]
NC_000011.9:g.6411936_6411941del
NC_000011.9:g.6411966_6411971delGCTGGC
NM_000543.4:c.120_125delGCTGGC
NM_000543.4:c.138_143del6
NM_000543.4:c.138_143delGCTGGC
NM_000543.5:c.138_143delMANE SELECT
NM_000543.5:c.138_143delGCTGGCMANE SELECT
NR_027400.3:n.233GCTGGC[5]
NR_134502.2:n.233GCTGGC[5]

Links:

dbSNP: rs3838786

NCBI 1000 Genomes Browser:

rs3838786

Molecular consequence:

NM_001318088.2:c.-854GCTGGC[5] - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000543.5:c.108GCTGGC[5] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001007593.3:c.108GCTGGC[5] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001318087.2:c.108GCTGGC[5] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001365135.2:c.108GCTGGC[5] - inframe_deletion - [Sequence Ontology: SO:0001822]
NR_027400.3:n.233GCTGGC[5] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_134502.2:n.233GCTGGC[5] - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000697411	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Benign (Sep 2, 2016)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 17360762, 25301364 LabCorp Variant Classification Summary - May 2015.docx, Citation Link,
SCV000801059	Mayo Clinic Laboratories, Mayo Clinic	no assertion criteria provided	Uncertain significance (Oct 22, 2015)	unknown	clinical testing
SCV001752329	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Benign (Jul 5, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000697411

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Benign
(Sep 2, 2016)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV000801059

Mayo Clinic Laboratories, Mayo Clinic

no assertion criteria provided

Uncertain significance
(Oct 22, 2015)

unknown

clinical testing

SCV001752329

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Benign
(Jul 5, 2018)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Highly variable neural involvement in sphingomyelinase-deficient Niemann-Pick disease caused by an ancestral Gypsy mutation.

Mihaylova V, Hantke J, Sinigerska I, Cherninkova S, Raicheva M, Bouwer S, Tincheva R, Khuyomdziev D, Bertranpetit J, Chandler D, Angelicheva D, Kremensky I, Seeman P, Tournev I, Kalaydjieva L.

Brain. 2007 Apr;130(Pt 4):1050-61. Epub 2007 Mar 14.

PubMed [citation]

PMID:: 17360762

Secretion of acid Sphingomyelinase is affected by its polymorphic signal peptide.

Rhein C, Reichel M, Mühle C, Rotter A, Schwab SG, Kornhuber J.

Cell Physiol Biochem. 2014;34(4):1385-401. doi: 10.1159/000366345. Epub 2014 Oct 2.

PubMed [citation]

PMID:: 25301364

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000697411.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

Variant summary: The SMPD1 c.138_143delGCTGGC (p.Leu47_Ala48del) variant involves an in-frame deletion of 6 nucleotides located in a known repeat region. Mutation taster predicts a benign outcome for this variant. This variant was found in 24716/110368 control chromosomes (6066 homozygotes), being most prevalent in the African subpopulation with a frequency of 0.3228346 (2706/8382). This frequency greatly exceeds the estimated maximal expected allele frequency of a pathogenic SMPD1 variant (0.0022361), suggesting this is likely a benign polymorphism found primarily in the populations of African origin. Multiple publications consider variant as a polymorphism. Considering the high frequency of the variant in the general population, it was classified as benign.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Mayo Clinic Laboratories, Mayo Clinic, SCV000801059.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From GeneDx, SCV001752329.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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