NM_000543.5(SMPD1):c.107_118del (p.Val36_Leu39del) AND multiple conditions

Germline classification:: Benign (1 submission)
Last evaluated:: Feb 1, 2024
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV001514585.15

Allele description [Variation Report for NM_000543.5(SMPD1):c.107_118del (p.Val36_Leu39del)]

NM_000543.5(SMPD1):c.107_118del (p.Val36_Leu39del)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

11p15.4

Genomic location:

Preferred name:

NM_000543.5(SMPD1):c.107_118del (p.Val36_Leu39del)

HGVS:

NC_000011.10:g.6390705_6390716del
NC_000011.9:g.6411931_6411942del
NG_011780.1:g.5281_5292del
NM_000543.4:c.107_118del12
NM_000543.5:c.107_118delMANE SELECT
NM_001007593.3:c.107_118del
NM_001318087.2:c.107_118del
NM_001318088.2:c.-855_-844del
NM_001365135.2:c.107_118del
NP_000534.3:p.Val36_Leu39del
NP_001007594.2:p.Val36_Leu39del
NP_001305016.1:p.Val36_Leu39del
NP_001352064.1:p.Val36_Leu39del
NC_000011.9:g.6411931_6411942del
NC_000011.9:g.6411935_6411946del
NC_000011.9:g.6411935_6411946del
NC_000011.9:g.6411935_6411946delTGCTGGCGCTGG
NM_000543.4:c.107_118del12
NM_000543.4:c.107_118delTGCTGGCGCTGG
NM_000543.5:c.107_118del
NR_027400.3:n.232_243del
NR_134502.2:n.232_243del

Links:

dbSNP: rs550365194

NCBI 1000 Genomes Browser:

rs550365194

Molecular consequence:

NM_001318088.2:c.-855_-844del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000543.5:c.107_118del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001007593.3:c.107_118del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001318087.2:c.107_118del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001365135.2:c.107_118del - inframe_deletion - [Sequence Ontology: SO:0001822]
NR_027400.3:n.232_243del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_134502.2:n.232_243del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Niemann-Pick disease, type B
Identifiers:: MONDO: MONDO:0011871; MedGen: C0268243; Orphanet: 77293; OMIM: 607616

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001722463	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Feb 1, 2024)	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

SCV001722463

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Feb 1, 2024)

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	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001722463.4

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

#	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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