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NM_000543.5(SMPD1):c.83C>T (p.Pro28Leu)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Mar 31, 2021)
Last evaluated:
Nov 11, 2020
Accession:
VCV000593169.6
Variation ID:
593169
Description:
single nucleotide variant
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NM_000543.5(SMPD1):c.83C>T (p.Pro28Leu)

Allele ID
584233
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11p15.4
Genomic location
11: 6390681 (GRCh38) GRCh38 UCSC
11: 6411911 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000011.10:g.6390681C>T
NC_000011.9:g.6411911C>T
NG_011780.1:g.5257C>T
... more HGVS
Protein change
P28L
Other names
-
Canonical SPDI
NC_000011.10:6390680:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00180 (T)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00001
The Genome Aggregation Database (gnomAD) 0.00003
Exome Aggregation Consortium (ExAC) 0.00074
1000 Genomes Project 0.00180
The Genome Aggregation Database (gnomAD), exomes 0.00058
Links
dbSNP: rs556155962
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Jul 10, 2017 RCV000728133.1
Benign 1 criteria provided, single submitter Nov 11, 2020 RCV000915596.3
Uncertain significance 1 criteria provided, single submitter Apr 27, 2017 RCV001107111.1
Uncertain significance 1 no assertion criteria provided - RCV001357849.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SMPD1 - - GRCh38
GRCh37
582 605

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Jul 10, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000855667.1
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Uncertain significance
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Niemann-Pick disease, type A
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001264242.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Benign
(Nov 11, 2020)
criteria provided, single submitter
Method: clinical testing
Niemann-Pick disease, type B
Niemann-Pick disease, type A
Allele origin: germline
Invitae
Accession: SCV001060811.3
Submitted: (Jan 07, 2021)
Evidence details
Uncertain significance
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: unknown
Department of Pathology and Laboratory Medicine,Sinai Health System
Additional submitter:
Franklin by Genoox
Study: The Canadian Open Genetics Repository (COGR)
Accession: SCV001553438.1
Submitted: (Mar 31, 2021)
Evidence details
Comment:
The SMPD1 p.Pro28Leu variant was not identified in the literature but was identified in dbSNP (ID: rs556155962) and ClinVar (classified as likely benign by EGL … (more)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=SMPD1 - - - -

Text-mined citations for rs556155962...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021