Variant 13-32385652-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000059.4(BRCA2):c.9256+5507T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 232,116 control chromosomes in the GnomAD database, including 5,307 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★★).

Frequency

Genomes: 𝑓 0.21 ( 3514 hom., cov: 32)

Exomes 𝑓: 0.21 ( 1793 hom. )

Consequence

BRCA2
NM_000059.4 intron

Scores

Clinical Significance

Benign reviewed by expert panel B:2

Conservation

PhyloP100: 0.370

Variant links:

Genes affected

BRCA2 (HGNC:1101): (BRCA2 DNA repair associated) Inherited mutations in BRCA1 and this gene, BRCA2, confer increased lifetime risk of developing breast or ovarian cancer. Both BRCA1 and BRCA2 are involved in maintenance of genome stability, specifically the homologous recombination pathway for double-strand DNA repair. The largest exon in both genes is exon 11, which harbors the most important and frequent mutations in breast cancer patients. The BRCA2 gene was found on chromosome 13q12.3 in human. The BRCA2 protein contains several copies of a 70 aa motif called the BRC motif, and these motifs mediate binding to the RAD51 recombinase which functions in DNA repair. BRCA2 is considered a tumor suppressor gene, as tumors with BRCA2 mutations generally exhibit loss of heterozygosity (LOH) of the wild-type allele. [provided by RefSeq, May 2020]

BRCA2 links:

IFIT1P1 (HGNC:):

IFIT1P1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.72).

BP6

Variant 13-32385652-T-C is Benign according to our data. Variant chr13-32385652-T-C is described in ClinVar as [Benign]. Clinvar id is 209872.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr13-32385652-T-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BRCA2	NM_000059.4 linkuse as main transcript	c.9256+5507T>C		intron_variant		ENST00000380152.8	NP_000050.3	P51587

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
BRCA2	ENST00000380152.8 linkuse as main transcript	c.9256+5507T>C	intron_variant	5	NM_000059.4	ENSP00000369497.3	P51587
BRCA2	ENST00000530893.7 linkuse as main transcript	c.8887+5507T>C	intron_variant	1		ENSP00000499438.2	A0A590UJI7
BRCA2	ENST00000614259.2 linkuse as main transcript	n.*1314+5507T>C	intron_variant	2		ENSP00000506251.1	A0A7P0TAP7

Frequencies

GnomAD3 genomes

AF:

0.213

AC:

32405

AN:

151966

Hom.:

3512

Cov.:

show subpopulations

Gnomad AFR

AF:

0.218

Gnomad AMI

AF:

0.280

Gnomad AMR

AF:

0.173

Gnomad ASJ

AF:

0.147

Gnomad EAS

AF:

0.247

Gnomad SAS

AF:

0.233

Gnomad FIN

AF:

0.223

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.216

Gnomad OTH

AF:

0.214

GnomAD4 exome

AF:

0.206

AC:

16509

AN:

80030

Hom.:

1793

Cov.:

AF XY:

0.207

AC XY:

9930

AN XY:

48038

show subpopulations

Gnomad4 AFR exome

AF:

0.210

Gnomad4 AMR exome

AF:

0.166

Gnomad4 ASJ exome

AF:

0.155

Gnomad4 EAS exome

AF:

0.203

Gnomad4 SAS exome

AF:

0.194

Gnomad4 FIN exome

AF:

0.210

Gnomad4 NFE exome

AF:

0.212

Gnomad4 OTH exome

AF:

0.187

GnomAD4 genome

AF:

0.213

AC:

32410

AN:

152086

Hom.:

3514

Cov.:

AF XY:

0.212

AC XY:

15760

AN XY:

74312

show subpopulations

Gnomad4 AFR

AF:

0.217

Gnomad4 AMR

AF:

0.173

Gnomad4 ASJ

AF:

0.147

Gnomad4 EAS

AF:

0.248

Gnomad4 SAS

AF:

0.233

Gnomad4 FIN

AF:

0.223

Gnomad4 NFE

AF:

0.216

Gnomad4 OTH

AF:

0.212

Alfa

AF:

0.144

Hom.:

363

Bravo

AF:

0.212

Asia WGS

AF:

0.211

AC:

735

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: reviewed by expert panel

LINK: link

Submissions by phenotype

Breast-ovarian cancer, familial, susceptibility to, 2

Benign:1

Benign, reviewed by expert panel

curation

Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA)

Jan 12, 2015

Class 1 not pathogenic based on frequency >1% in an outbred sampleset. Frequency 0.2587 (Asian), 0.2195 (African), 0.2137 (European), derived from 1000 genomes (2012-04-30). -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

0.43

DANN

Benign

0.52

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over