2-214767531-CA-TG

Variant names:

• chr2-214767531-CA-TG
• rs386654966
• NM_000465.4:c.1518_1519delTGinsCA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP6_Very_Strong

The NM_000465.4(BARD1):​c.1518_1519delTGinsCA​(p.Val507Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. HV506PM) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: BARD1 NM_000465.4 missense
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts U:1 B:9
• Conservation: PhyloP100: -0.241
• Publications: 7 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: Benign. The variant received -8 ACMG points.

• BP6: Variant 2-214767531-CA-TG is Benign according to our data. Variant chr2-214767531-CA-TG is described in CliVar as Benign/Likely_benign. Clinvar id is 215471.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-214767531-CA-TG is described in CliVar as Benign/Likely_benign. Clinvar id is 215471.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-214767531-CA-TG is described in CliVar as Benign/Likely_benign. Clinvar id is 215471.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-214767531-CA-TG is described in CliVar as Benign/Likely_benign. Clinvar id is 215471.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-214767531-CA-TG is described in CliVar as Benign/Likely_benign. Clinvar id is 215471.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-214767531-CA-TG is described in CliVar as Benign/Likely_benign. Clinvar id is 215471.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-214767531-CA-TG is described in CliVar as Benign/Likely_benign. Clinvar id is 215471.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-214767531-CA-TG is described in CliVar as Benign/Likely_benign. Clinvar id is 215471.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-214767531-CA-TG is described in CliVar as Benign/Likely_benign. Clinvar id is 215471.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-214767531-CA-TG is described in CliVar as Benign/Likely_benign. Clinvar id is 215471.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-214767531-CA-TG is described in CliVar as Benign/Likely_benign. Clinvar id is 215471.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-214767531-CA-TG is described in CliVar as Benign/Likely_benign. Clinvar id is 215471.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-214767531-CA-TG is described in CliVar as Benign/Likely_benign. Clinvar id is 215471.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-214767531-CA-TG is described in CliVar as Benign/Likely_benign. Clinvar id is 215471.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-214767531-CA-TG is described in CliVar as Benign/Likely_benign. Clinvar id is 215471.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-214767531-CA-TG is described in CliVar as Benign/Likely_benign. Clinvar id is 215471.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.1518_1519delTGinsCA	p.Val507Met	missense_variant		ENST00000260947.9	NP_000456.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BARD1	ENST00000260947.9	c.1518_1519delTGinsCA	p.Val507Met	missense_variant		1	NM_000465.4	ENSP00000260947.4

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Significance: Benign/Likely benign

Submissions summary: Uncertain:1 Benign:9

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Familial cancer of breast Benign:5

Jul 07, 2023

KCCC/NGS Laboratory, Kuwait Cancer Control Center

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 01, 2019

Institute of Human Genetics, University of Leipzig Medical Center

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jul 25, 2024

Myriad Genetics, Inc.

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered benign. This variant has been observed at a population frequency that is significantly greater than expected given the associated disease prevalence and penetrance. -

Nov 26, 2024

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hereditary cancer-predisposing syndrome Benign:2

Jun 03, 2025

Ambry Genetics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Jul 10, 2015

Color Diagnostics, LLC DBA Color Health

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breast carcinoma Uncertain:1

Aug 20, 2021

Medical Genetics Laboratory, Umraniye Training and Research Hospital, University of Health Sciences

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

Invasive Ductal Carcinoma Estrogen Receptor: Positive Progesterone Receptor: Positive HER2 Receptor: Positive -

not specified Benign:1

Oct 03, 2016

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hereditary breast ovarian cancer syndrome Benign:1

Apr 19, 2022

National Health Laboratory Service, Universitas Academic Hospital and University of the Free State

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.24
Mutation Taster		=77/23	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs386654966; hg19: chr2-215632255; COSMIC: COSV105837301;