NM_000543.5(SMPD1):c.107_112del (p.Val36_Leu37del) AND not provided

Germline classification:: Likely benign (3 submissions)
Last evaluated:: Jul 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:: RCV001729484.11

Allele description [Variation Report for NM_000543.5(SMPD1):c.107_112del (p.Val36_Leu37del)]

NM_000543.5(SMPD1):c.107_112del (p.Val36_Leu37del)

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_112del (p.Val36_Leu37del)

HGVS:

NC_000011.10:g.6390705_6390710del
NG_011780.1:g.5281_5286del
NM_000543.5:c.107_112delMANE SELECT
NM_001007593.3:c.107_112del
NM_001318087.2:c.107_112del
NM_001318088.2:c.-855_-850del
NM_001365135.2:c.107_112del
NP_000534.3:p.Val36_Leu37del
NP_001007594.2:p.Val36_Leu37del
NP_001305016.1:p.Val36_Leu37del
NP_001352064.1:p.Val36_Leu37del
NC_000011.9:g.6411931_6411936del
NC_000011.9:g.6411935_6411940del
NM_000543.4:c.107_112del
NM_000543.4:c.107_112del6
NM_000543.4:c.107_112delTGCTGG
NR_027400.3:n.232_237del
NR_134502.2:n.232_237del

Links:

dbSNP: rs775860642

NCBI 1000 Genomes Browser:

rs775860642

Molecular consequence:

NM_001318088.2:c.-855_-850del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000543.5:c.107_112del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001007593.3:c.107_112del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001318087.2:c.107_112del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001365135.2:c.107_112del - inframe_deletion - [Sequence Ontology: SO:0001822]
NR_027400.3:n.232_237del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_134502.2:n.232_237del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Homo sapiens beta-galactose-3-O-sulfotransferase, 4 (GAL3ST-4), mRNA
Homo sapiens beta-galactose-3-O-sulfotransferase, 4 (GAL3ST-4), mRNA
gi|20127626|ref|NM_024637.2|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001978708	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus	no assertion criteria provided	Likely benign	germline	clinical testing
SCV001980388	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Likely benign	germline	clinical testing
SCV004135837	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Likely benign (Jul 1, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001978708

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus

no assertion criteria provided

Likely benign

germline

clinical testing

SCV001980388

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided

Likely benign

germline

clinical testing

SCV004135837

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Likely benign
(Jul 1, 2024)

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	4	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV001978708.1

#	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

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV001980388.1

#	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

From CeGaT Center for Human Genetics Tuebingen, SCV004135837.10

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	4	not provided	not provided	clinical testing	not provided

Description

SMPD1: PM4, BS2

#	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		4	not provided	not provided	not provided

Last Updated: Oct 20, 2024

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