NM_000543.5(SMPD1):c.107T>C (p.Val36Ala) AND not specified

Germline classification:: Benign (2 submissions)
Last evaluated:: Feb 1, 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:: RCV000079189.24

Allele description [Variation Report for NM_000543.5(SMPD1):c.107T>C (p.Val36Ala)]

NM_000543.5(SMPD1):c.107T>C (p.Val36Ala)

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.107T>C (p.Val36Ala)

HGVS:

NC_000011.10:g.6390705T>C
NG_011780.1:g.5281T>C
NM_000543.5:c.107T>CMANE SELECT
NM_001007593.3:c.107T>C
NM_001318087.2:c.107T>C
NM_001318088.2:c.-855T>C
NM_001365135.2:c.107T>C
NP_000534.3:p.Val36Ala
NP_000534.3:p.Val36Ala
NP_001007594.2:p.Val36Ala
NP_001305016.1:p.Val36Ala
NP_001352064.1:p.Val36Ala
NC_000011.9:g.6411935T>C
NM_000543.4:c.107T>C
NR_027400.3:n.232T>C
NR_134502.2:n.232T>C

Protein change:

V36A

Links:

dbSNP: rs1050228

NCBI 1000 Genomes Browser:

rs1050228

Molecular consequence:

NM_001318088.2:c.-855T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000543.5:c.107T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001007593.3:c.107T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001318087.2:c.107T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001365135.2:c.107T>C - missense variant - [Sequence Ontology: SO:0001583]
NR_027400.3:n.232T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_134502.2:n.232T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

168

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

Recent activity

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Homo sapiens SPOC domain containing 1 (SPOCD1), mRNA
Homo sapiens SPOC domain containing 1 (SPOCD1), mRNA
gi|142366582|ref|NM_144569.4|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000111058	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Benign (Feb 1, 2018)	germline	clinical testing	Citation Link,
SCV000540391	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Benign (Mar 28, 2016)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000111058

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions 2015)

Benign
(Feb 1, 2018)

germline

clinical testing

Citation Link,

SCV000540391

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Benign
(Mar 28, 2016)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	168	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]

PMID:: 24033266
PMCID:: PMC3995020

Details of each submission

From Eurofins Ntd Llc (ga), SCV000111058.8

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	168	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	unknown	not provided	not provided	not provided		168	not provided	not provided	not provided

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000540391.1

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

Description

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: MAF

#	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

Last Updated: Nov 3, 2024

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