chr2-214792454-T-A

Variant names:

• chr2-214792454-T-A
• rs759575504
• NM_000465.4:c.216-9A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BP6_Very_Strong

The NM_000465.4(BARD1):​c.216-9A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0013 (0 hom., cov: 28)
  • Exomes 𝑓: 0.0037 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: BARD1 NM_000465.4 intron
• Scores: Splicing: ADA: 0.00002109
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:6
• Conservation: PhyloP100: -0.559
• Publications: 0 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):

• BARD1-related cancer predisposition

  Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
• breast cancer

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

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

  Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 2-214792454-T-A is Benign according to our data. Variant chr2-214792454-T-A is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 489669.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000465.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BARD1	NM_000465.4	MANE Select	c.216-9A>T		intron	N/A	NP_000456.2	Q99728-1
	BARD1	NM_001282543.2		c.159-9A>T		intron	N/A	NP_001269472.1	Q99728-2
	BARD1	NM_001282545.2		c.215+4607A>T		intron	N/A	NP_001269474.1	C9IYG1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BARD1	ENST00000260947.9	TSL:1 MANE Select	c.216-9A>T		intron	N/A	ENSP00000260947.4	Q99728-1
	BARD1	ENST00000617164.5	TSL:1	c.159-9A>T		intron	N/A	ENSP00000480470.1	Q99728-2
	BARD1	ENST00000613706.5	TSL:1	c.216-9A>T		intron	N/A	ENSP00000484976.2	A0A087X2H0

Frequencies

GnomAD3 genomes AF: 0.00134 AC: 140 AN: 104426 Hom.: 0 Cov.: 28

Gnomad AFR AF: 0.00114

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000691

Gnomad ASJ AF: 0.000782

Gnomad EAS AF: 0.000791

Gnomad SAS AF: 0.000922

Gnomad FIN AF: 0.00309

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00153

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.0355 AC: 1960 AN: 55262 AF XY: 0.0343

Gnomad AFR exome AF: 0.0281

Gnomad AMR exome AF: 0.0102

Gnomad ASJ exome AF: 0.0240

Gnomad EAS exome AF: 0.0174

Gnomad FIN exome AF: 0.126

Gnomad NFE exome AF: 0.0406

Gnomad OTH exome AF: 0.0293

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00365 AC: 4712 AN: 1289906 Hom.: 0 Cov.: 33 AF XY: 0.00459 AC XY: 2910 AN XY: 633326

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00108 AC: 29 AN: 26874

American (AMR) AF: 0.0124 AC: 292 AN: 23480

Ashkenazi Jewish (ASJ) AF: 0.0123 AC: 255 AN: 20768

East Asian (EAS) AF: 0.00242 AC: 76 AN: 31386

South Asian (SAS) AF: 0.0170 AC: 1006 AN: 59266

European-Finnish (FIN) AF: 0.0354 AC: 1208 AN: 34114

Middle Eastern (MID) AF: 0.00273 AC: 11 AN: 4024

European-Non Finnish (NFE) AF: 0.00164 AC: 1702 AN: 1036804

Other (OTH) AF: 0.00250 AC: 133 AN: 53190

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00134 AC: 140 AN: 104442 Hom.: 0 Cov.: 28 AF XY: 0.00153 AC XY: 77 AN XY: 50390

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00110 AC: 30 AN: 27296

American (AMR) AF: 0.000790 AC: 8 AN: 10130

Ashkenazi Jewish (ASJ) AF: 0.000782 AC: 2 AN: 2558

East Asian (EAS) AF: 0.000794 AC: 3 AN: 3778

South Asian (SAS) AF: 0.000928 AC: 3 AN: 3234

European-Finnish (FIN) AF: 0.00309 AC: 19 AN: 6148

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 188

European-Non Finnish (NFE) AF: 0.00153 AC: 75 AN: 49006

Other (OTH) AF: 0.00 AC: 0 AN: 1428

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00153 Hom.: 0

ClinVar

ClinVar submissions

Significance: Benign/Likely benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	Hereditary cancer-predisposing syndrome (2)
-	-	2	not specified (2)
-	-	1	Familial cancer of breast (1)
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.17
DANN	Benign	0.74
PhyloP100		-0.56
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000021
dbscSNV1_RF	Benign	0.0020
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: rs759575504; hg19: chr2-215657178;