chr2-214745151-CAT-C

Variant names:

• chr2-214745151-CAT-C
• rs587782897
• NM_000465.4:c.1817_1818delAT

Variant summary

Our verdict is Pathogenic. The variant received 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_000465.4(BARD1):​c.1817_1818delAT​(p.His606ArgfsTer6) variant causes a frameshift change. The variant allele was found at a frequency of 0.00000657 in 152,134 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. H606H) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: 𝑓 0.0000066 (0 hom., cov: 33)
• Consequence: BARD1 NM_000465.4 frameshift
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:7
• Conservation: PhyloP100: 5.50
• Publications: 3 publications found

Genes affected

BARD1 (HGNC:952): (BRCA1 associated RING domain 1) This gene encodes a protein which interacts with the N-terminal region of BRCA1. In addition to its ability to bind BRCA1 in vivo and in vitro, it shares homology with the 2 most conserved regions of BRCA1: the N-terminal RING motif and the C-terminal BRCT domain. The RING motif is a cysteine-rich sequence found in a variety of proteins that regulate cell growth, including the products of tumor suppressor genes and dominant protooncogenes. This protein also contains 3 tandem ankyrin repeats. The BARD1/BRCA1 interaction is disrupted by tumorigenic amino acid substitutions in BRCA1, implying that the formation of a stable complex between these proteins may be an essential aspect of BRCA1 tumor suppression. This protein may be the target of oncogenic mutations in breast or ovarian cancer. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2013]

BARD1 Gene-Disease associations (from GenCC):

• breast cancer

  Inheritance: AD Classification: DEFINITIVE Submitted by: G2P
• hereditary breast carcinoma

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), ClinGen
• familial ovarian cancer

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen
• hereditary nonpolyposis colon cancer

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen

ACMG classification

Our verdict: Pathogenic. The variant received 18 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 2-214745151-CAT-C is Pathogenic according to our data. Variant chr2-214745151-CAT-C is described in CliVar as Pathogenic. Clinvar id is 143017.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-214745151-CAT-C is described in CliVar as Pathogenic. Clinvar id is 143017.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-214745151-CAT-C is described in CliVar as Pathogenic. Clinvar id is 143017.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-214745151-CAT-C is described in CliVar as Pathogenic. Clinvar id is 143017.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-214745151-CAT-C is described in CliVar as Pathogenic. Clinvar id is 143017.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-214745151-CAT-C is described in CliVar as Pathogenic. Clinvar id is 143017.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-214745151-CAT-C is described in CliVar as Pathogenic. Clinvar id is 143017.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-214745151-CAT-C is described in CliVar as Pathogenic. Clinvar id is 143017.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-214745151-CAT-C is described in CliVar as Pathogenic. Clinvar id is 143017.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-214745151-CAT-C is described in CliVar as Pathogenic. Clinvar id is 143017.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-214745151-CAT-C is described in CliVar as Pathogenic. Clinvar id is 143017.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-214745151-CAT-C is described in CliVar as Pathogenic. Clinvar id is 143017.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-214745151-CAT-C is described in CliVar as Pathogenic. Clinvar id is 143017.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-214745151-CAT-C is described in CliVar as Pathogenic. Clinvar id is 143017.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-214745151-CAT-C is described in CliVar as Pathogenic. Clinvar id is 143017.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-214745151-CAT-C is described in CliVar as Pathogenic. Clinvar id is 143017.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BARD1	NM_000465.4	c.1817_1818delAT	p.His606ArgfsTer6	frameshift_variant	Exon 9 of 11	ENST00000260947.9	NP_000456.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BARD1	ENST00000260947.9	c.1817_1818delAT	p.His606ArgfsTer6	frameshift_variant	Exon 9 of 11	1	NM_000465.4	ENSP00000260947.4

Frequencies

GnomAD3 genomes AF: 0.00000657 AC: 1 AN: 152134 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.00000657 AC: 1 AN: 152134 Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0 AN XY: 74312

African (AFR) AF: 0.00 AC: 0 AN: 41428

American (AMR) AF: 0.00 AC: 0 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3462

East Asian (EAS) AF: 0.00 AC: 0 AN: 5192

South Asian (SAS) AF: 0.00 AC: 0 AN: 4828

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10602

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.0000147 AC: 1 AN: 68026

Other (OTH) AF: 0.00 AC: 0 AN: 2090

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:7

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Familial cancer of breast Pathogenic:3

May 24, 2023

Myriad Genetics, Inc.

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation. -

Jan 08, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change creates a premature translational stop signal (p.His606Argfs*6) in the BARD1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in BARD1 are known to be pathogenic (PMID: 20077502, 21344236). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with BARD1-related conditions. ClinVar contains an entry for this variant (Variation ID: 143017). For these reasons, this variant has been classified as Pathogenic. -

Nov 02, 2023

Baylor Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hereditary cancer-predisposing syndrome Pathogenic:2

Apr 15, 2024

Color Diagnostics, LLC DBA Color Health

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant deletes 2 nucleotides in exon 9 of the BARD1 gene, creating a frameshift and premature translation stop signal. This variant is expected to result in an absent or non-functional protein product. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of BARD1 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic. -

Mar 22, 2024

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1817_1818delAT pathogenic mutation, located in coding exon 9 of the BARD1 gene, results from a deletion of two nucleotides at nucleotide positions 1817 to 1818, causing a translational frameshift with a predicted alternate stop codon (p.H606Rfs*6). This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. -

BARD1-related disorder Pathogenic:1

May 12, 2024

PreventionGenetics, part of Exact Sciences

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

The BARD1 c.1817_1818delAT variant is predicted to result in a frameshift and premature protein termination (p.His606Argfs*6). To our knowledge, this variant has not been reported in a patient with a BARD1 related disorder. This variant has not been reported in a large population database, indicating this variant is rare. This variant is interpreted as pathogenic in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/143017/). Frameshift variants in BARD1 are expected to be pathogenic. This variant is interpreted as likely pathogenic. -

not provided Pathogenic:1

Jul 13, 2022

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; Observed in an individual undergoing clinical exome testing for unspecified history and classified as pathogenic (LaDuca et al., 2017); This variant is associated with the following publications: (PMID: 28152038) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		5.5
Mutation Taster		=0/200	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs587782897; hg19: chr2-215609875;