2-214728552-TGA-T
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_000465.4(BARD1):c.*122_*123del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000401 in 760,112 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00075 ( 0 hom., cov: 18)
Exomes 𝑓: 0.00040 ( 1 hom. )
Failed GnomAD Quality Control
Consequence
BARD1
NM_000465.4 3_prime_UTR
NM_000465.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.114
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 Likely_benign. Variant got -6 ACMG points.
BP6
Variant 2-214728552-TGA-T is Benign according to our data. Variant chr2-214728552-TGA-T is described in ClinVar as [Benign]. Clinvar id is 801876.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAdExome4 at 305 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BARD1 | NM_000465.4 | c.*122_*123del | 3_prime_UTR_variant | 11/11 | ENST00000260947.9 | NP_000456.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BARD1 | ENST00000260947.9 | c.*122_*123del | 3_prime_UTR_variant | 11/11 | 1 | NM_000465.4 | ENSP00000260947 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 113AN: 150372Hom.: 0 Cov.: 18 FAILED QC
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GnomAD4 exome AF: 0.000401 AC: 305AN: 760112Hom.: 1 AF XY: 0.000431 AC XY: 167AN XY: 387156
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000751 AC: 113AN: 150486Hom.: 0 Cov.: 18 AF XY: 0.000626 AC XY: 46AN XY: 73528
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Data not reliable, filtered out with message: AS_VQSR
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Familial cancer of breast Benign:1
Benign, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at