NM_004287.5(GOSR2):c.29+1G>A AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Dec 24, 2015
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:: RCV000255066.1

Allele description [Variation Report for NM_004287.5(GOSR2):c.29+1G>A]

NM_004287.5(GOSR2):c.29+1G>A

Genes:

GOSR2:golgi SNAP receptor complex member 2 [Gene - OMIM - HGNC]
LRRC37A2:leucine rich repeat containing 37 member A2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17q21.32

Genomic location:

Preferred name:

NM_004287.5(GOSR2):c.29+1G>A

HGVS:

NC_000017.11:g.46923222G>A
NG_031806.2:g.5103G>A
NG_031806.3:g.5064G>A
NG_136814.1:g.187G>A
NM_001012511.3:c.29+1G>A
NM_001321133.2:c.29+1G>A
NM_001321134.2:c.-73G>A
NM_001330252.2:c.29+1G>A
NM_001353114.2:c.29+1G>A
NM_001353115.2:c.29+1G>A
NM_001353116.2:c.29+1G>A
NM_001363851.2:c.-436G>A
NM_004287.5:c.29+1G>AMANE SELECT
NM_054022.4:c.29+1G>A
NC_000017.10:g.45000588G>A
NM_004287.3:c.29+1G>A

Links:

dbSNP: rs886039603

NCBI 1000 Genomes Browser:

rs886039603

Molecular consequence:

NM_001321134.2:c.-73G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001363851.2:c.-436G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001012511.3:c.29+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001321133.2:c.29+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001330252.2:c.29+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001353114.2:c.29+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001353115.2:c.29+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001353116.2:c.29+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_004287.5:c.29+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_054022.4:c.29+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000322507	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Likely pathogenic (Dec 24, 2015)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000322507

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Likely pathogenic
(Dec 24, 2015)

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

Details of each submission

From GeneDx, SCV000322507.7

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

Description

The c.29+1 G>A likely pathogenic variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. It was not observed in approximately 5,000 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The c.29+1 G>A splice site variant destroys the canonical splice donor site in intron 1. It is predicted to cause abnormal gene splicing, either leading to an abnormal message that is subject to nonsense-mediated mRNA decay, or to an abnormal protein product if the message is used for protein translation. Therefore, this variant is likely pathogenic; however, the possibility that it is benign cannot be excluded.

#	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: Jun 10, 2023

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