NM_000059.4:c.9501+178A>G

Variant names:

• chr13-32395111-A-G
• rs206343
• NM_000059.4:c.9501+178A>G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_000059.4(BRCA2):​c.9501+178A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,184 control chromosomes in the GnomAD database, including 2,340 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★★).

• Frequency: Genomes: 𝑓 0.16 (2340 hom., cov: 32)
• Consequence: BRCA2 NM_000059.4 intron
• Clinical Significance: Benign reviewed by expert panel B:2
• Conservation: PhyloP100: -0.865

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]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 13-32395111-A-G is Benign according to our data. Variant chr13-32395111-A-G is described in ClinVar as [Benign]. Clinvar id is 209911.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr13-32395111-A-G is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRCA2	NM_000059.4	c.9501+178A>G		intron_variant	Intron 25 of 26	ENST00000380152.8	NP_000050.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BRCA2	ENST00000380152.8	c.9501+178A>G		intron_variant	Intron 25 of 26	5	NM_000059.4	ENSP00000369497.3
BRCA2	ENST00000530893.7	c.9132+178A>G		intron_variant	Intron 25 of 26	1		ENSP00000499438.2
BRCA2	ENST00000614259.2	n.*1559+178A>G		intron_variant	Intron 24 of 25	2		ENSP00000506251.1

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23780 AN: 152066 Hom.: 2342 Cov.: 32

Gnomad AFR AF: 0.0429

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.156 AC: 23771 AN: 152184 Hom.: 2340 Cov.: 32 AF XY: 0.156 AC XY: 11623 AN XY: 74414

Gnomad4 AFR AF: 0.0427

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.224

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.165

Alfa AF: 0.172 Hom.: 324

Bravo AF: 0.144

Asia WGS AF: 0.182 AC: 634 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: reviewed by expert panel

Submissions by phenotype

Breast-ovarian cancer, familial, susceptibility to, 2 Benign:1

Jan 12, 2015

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

Significance: Benign

Review Status: reviewed by expert panel

Collection Method: curation

Class 1 not pathogenic based on frequency >1% in an outbred sampleset. Frequency 0.229 (Asian), 0.01626 (African), 0.2111 (European), derived from 1000 genomes (2012-04-30). -

not provided Benign:1

Jun 22, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.99
DANN	Benign	0.76

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

Other links and lift over

dbSNP: rs206343; hg19: chr13-32969248;