2-214728537-CT-C

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_000465.4(BARD1):​c.*138del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.068 ( 444 hom., cov: 0)
Exomes 𝑓: 0.077 ( 57 hom. )

Consequence

BARD1
NM_000465.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.392
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6
Variant 2-214728537-CT-C is Benign according to our data. Variant chr2-214728537-CT-C is described in ClinVar as [Benign]. Clinvar id is 801875.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
BARD1NM_000465.4 linkuse as main transcriptc.*138del 3_prime_UTR_variant 11/11 ENST00000260947.9 NP_000456.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
BARD1ENST00000260947.9 linkuse as main transcriptc.*138del 3_prime_UTR_variant 11/111 NM_000465.4 ENSP00000260947 P2Q99728-1

Frequencies

GnomAD3 genomes
AF:
0.0679
AC:
9778
AN:
143932
Hom.:
444
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.133
Gnomad AMI
AF:
0.0487
Gnomad AMR
AF:
0.0440
Gnomad ASJ
AF:
0.0579
Gnomad EAS
AF:
0.000200
Gnomad SAS
AF:
0.0137
Gnomad FIN
AF:
0.0216
Gnomad MID
AF:
0.0617
Gnomad NFE
AF:
0.0495
Gnomad OTH
AF:
0.0635
GnomAD4 exome
AF:
0.0766
AC:
33059
AN:
431740
Hom.:
57
Cov.:
6
AF XY:
0.0761
AC XY:
17034
AN XY:
223748
show subpopulations
Gnomad4 AFR exome
AF:
0.146
Gnomad4 AMR exome
AF:
0.0788
Gnomad4 ASJ exome
AF:
0.0824
Gnomad4 EAS exome
AF:
0.0333
Gnomad4 SAS exome
AF:
0.0601
Gnomad4 FIN exome
AF:
0.0453
Gnomad4 NFE exome
AF:
0.0810
Gnomad4 OTH exome
AF:
0.0847
GnomAD4 genome
AF:
0.0680
AC:
9790
AN:
143958
Hom.:
444
Cov.:
0
AF XY:
0.0649
AC XY:
4516
AN XY:
69622
show subpopulations
Gnomad4 AFR
AF:
0.133
Gnomad4 AMR
AF:
0.0439
Gnomad4 ASJ
AF:
0.0579
Gnomad4 EAS
AF:
0.000201
Gnomad4 SAS
AF:
0.0136
Gnomad4 FIN
AF:
0.0216
Gnomad4 NFE
AF:
0.0495
Gnomad4 OTH
AF:
0.0631

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxAug 09, 2019- -
Familial cancer of breast Benign:1
Benign, criteria provided, single submitterclinical testingMendelicsMay 28, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs113789798; hg19: chr2-215593261; API