NM_000465.4(BARD1):c.1872del (p.Leu625fs) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Nov 1, 2018
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:: RCV000479681.22

Allele description [Variation Report for NM_000465.4(BARD1):c.1872del (p.Leu625fs)]

NM_000465.4(BARD1):c.1872del (p.Leu625fs)

Gene:

BARD1:BRCA1 associated RING domain 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

2q35

Genomic location:

Preferred name:

NM_000465.4(BARD1):c.1872del (p.Leu625fs)

HGVS:

NC_000002.12:g.214745099del
NG_012047.3:g.69614del
NM_000465.4:c.1872delMANE SELECT
NM_001282543.2:c.1815del
NM_001282545.2:c.519del
NM_001282548.2:c.462del
NM_001282549.2:c.365-14590del
NP_000456.2:p.Leu625fs
NP_001269472.1:p.Leu606fs
NP_001269474.1:p.Leu174fs
NP_001269477.1:p.Leu155fs
LRG_297t1:c.1872del
LRG_297:g.69614del
LRG_297p1:p.Leu625fs
NC_000002.11:g.215609822del
NC_000002.11:g.215609823del
NG_012047.2:g.69607del
NM_000465.2:c.1872delT
NM_000465.3:c.1872del
NM_000465.3:c.1872delT
NR_104212.2:n.1837del
NR_104215.2:n.1780del
NR_104216.2:n.1036del

Protein change:

L155fs

Links:

dbSNP: rs876659572

NCBI 1000 Genomes Browser:

rs876659572

Molecular consequence:

NM_000465.4:c.1872del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001282543.2:c.1815del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001282545.2:c.519del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001282548.2:c.462del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001282549.2:c.365-14590del - intron variant - [Sequence Ontology: SO:0001627]
NR_104212.2:n.1837del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_104215.2:n.1780del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_104216.2:n.1036del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000566887	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Jul 26, 2016)	germline	clinical testing	Citation Link,
SCV001247081	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Nov 1, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000566887

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Jul 26, 2016)

germline

clinical testing

Citation Link,

SCV001247081

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

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

Pathogenic
(Nov 1, 2018)

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	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000566887.3

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

Description

This deletion of one nucleotide in BARD1 is denoted c.1872delT at the cDNA level and p.Leu625SerfsX7 (L625SfsX7) at the protein level. The normal sequence, with the base that is deleted in braces, is GGAT[T]CTCA. The deletion causes a frameshift, which changes a Leucine to a Serine at codon 625, and creates a premature stop codon at position 7 of the new reading frame. Although this variant has not, to our knowledge, been reported in the literature, it is predicted to cause loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay. We consider this variant to be pathogenic.

#	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, SCV001247081.24

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

Last Updated: Aug 4, 2024

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