NM_032043.3(BRIP1):c.3412G>A (p.Asp1138Asn) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Jul 26, 2023
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:: RCV000587926.5

Allele description [Variation Report for NM_032043.3(BRIP1):c.3412G>A (p.Asp1138Asn)]

NM_032043.3(BRIP1):c.3412G>A (p.Asp1138Asn)

Gene:

BRIP1:BRCA1 interacting DNA helicase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17q23.2

Genomic location:

Preferred name:

NM_032043.3(BRIP1):c.3412G>A (p.Asp1138Asn)

HGVS:

NC_000017.11:g.61683634C>T
NG_007409.2:g.184926G>A
NM_032043.3:c.3412G>AMANE SELECT
NP_114432.2:p.Asp1138Asn
NP_114432.2:p.Asp1138Asn
LRG_300t1:c.3412G>A
LRG_300:g.184926G>A
LRG_300p1:p.Asp1138Asn
NC_000017.10:g.59760995C>T
NM_032043.2:c.3412G>A

Protein change:

D1138N

Links:

dbSNP: rs587780249

NCBI 1000 Genomes Browser:

rs587780249

Molecular consequence:

NM_032043.3:c.3412G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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acidic amino acid decarboxylase GADL1 isoform X2 [Gallus gallus]
acidic amino acid decarboxylase GADL1 isoform X2 [Gallus gallus]
gi|2201652800|ref|XP_046793936.1|

Protein
PREDICTED: Gallus gallus glutamate decarboxylase like 1 (GADL1), transcript vari...
PREDICTED: Gallus gallus glutamate decarboxylase like 1 (GADL1), transcript variant X1, mRNA
gi|2201652795|ref|XM_004939424.5|

Nucleotide
Homologene neighbors for GEO Profiles (Select 122554571) (0)
GEO Profiles
Chromosome neighbors for GEO Profiles (Select 122562864) (19)
GEO Profiles
Concise Conserved Domain Links for Protein (Select 1389892528) (3)
Conserved Domains

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000699723	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (Jul 15, 2016)	germline	clinical testing	LabCorp Variant Classification Summary - May 2015.docx, Citation Link,
SCV002319006	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Jul 26, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000699723

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(Jul 15, 2016)

germline

clinical testing

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV002319006

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Jul 26, 2023)

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
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000699723.1

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

Description

Variant summary: The BRIP1 c.3412G>A (p.Asp1138Asn) variant involves the alteration of a conserved nucleotide. 3/5 in silico tools predict a benign outcome. 4/5 splice prediction tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. This variant was found in 1/120914 control chromosomes, which does not rule out the pathogenicity of this variant. The variant of interest has not, to our knowledge, been reported in affected individuals via publications; nor evaluated for functional impact by in vivo/vitro studies. In addition, one clinical diagnostic laboratory classified this variant as VUS. Because of the absence of clinical information and the lack of functional studies, the variant was classified as a variant of uncertain significance (VUS) until additional information becomes available.

#	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

From GeneDx, SCV002319006.3

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

Description

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Observed in a patient with breast cancer (Guindalini et al., 2022); This variant is associated with the following publications: (PMID: 20159562, 21127055, 35264596)

#	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: Sep 29, 2024

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