chr17-43090832-G-T

Position:

• chr17-43090832-G-T

Variant summary

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

The NM_007294.4(BRCA1):​c.4185+112C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0233 in 1,003,540 control chromosomes in the GnomAD database, including 2,432 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★★).

• Frequency:
  • Genomes: 𝑓 0.025 (328 hom., cov: 32)
  • Exomes 𝑓: 0.023 (2104 hom.)
• Consequence: BRCA1 NM_007294.4 intron
• Clinical Significance: Benign reviewed by expert panel B:3
• Conservation: PhyloP100: -0.176

Genes affected

BRCA1 (HGNC:1100): (BRCA1 DNA repair associated) This gene encodes a 190 kD nuclear phosphoprotein that plays a role in maintaining genomic stability, and it also acts as a tumor suppressor. The BRCA1 gene contains 22 exons spanning about 110 kb of DNA. The encoded protein combines with other tumor suppressors, DNA damage sensors, and signal transducers to form a large multi-subunit protein complex known as the BRCA1-associated genome surveillance complex (BASC). This gene product associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. This protein thus plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers. Alternative splicing plays a role in modulating the subcellular localization and physiological function of this gene. Many alternatively spliced transcript variants, some of which are disease-associated mutations, have been described for this gene, but the full-length natures of only some of these variants has been described. A related pseudogene, which is also located on chromosome 17, has been identified. [provided by RefSeq, May 2020]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 17-43090832-G-T is Benign according to our data. Variant chr17-43090832-G-T is described in ClinVar as [Benign]. Clinvar id is 209443.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr17-43090832-G-T is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRCA1	NM_007294.4	c.4185+112C>A		intron_variant		ENST00000357654.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRCA1	ENST00000357654.9	c.4185+112C>A		intron_variant		1	NM_007294.4	P4

Frequencies

GnomAD3 genomes AF: 0.0247 AC: 3755 AN: 152136 Hom.: 324 Cov.: 32

Gnomad AFR AF: 0.00244

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0184

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.0159

Gnomad FIN AF: 0.0377

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00209

Gnomad OTH AF: 0.0234

GnomAD4 exome AF: 0.0231 AC: 19646 AN: 851286 Hom.: 2104 AF XY: 0.0210 AC XY: 9258 AN XY: 440038

Gnomad4 AFR exome AF: 0.00175

Gnomad4 AMR exome AF: 0.177

Gnomad4 ASJ exome AF: 0.0146

Gnomad4 EAS exome AF: 0.279

Gnomad4 SAS exome AF: 0.00790

Gnomad4 FIN exome AF: 0.0398

Gnomad4 NFE exome AF: 0.00130

Gnomad4 OTH exome AF: 0.0255

GnomAD4 genome AF: 0.0247 AC: 3763 AN: 152254 Hom.: 328 Cov.: 32 AF XY: 0.0290 AC XY: 2161 AN XY: 74460

Gnomad4 AFR AF: 0.00243

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.0184

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.0157

Gnomad4 FIN AF: 0.0377

Gnomad4 NFE AF: 0.00209

Gnomad4 OTH AF: 0.0237

Alfa AF: 0.0125 Hom.: 10

Bravo AF: 0.0328

Asia WGS AF: 0.111 AC: 387 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: reviewed by expert panel

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 26, 2018	- -

Breast-ovarian cancer, familial, susceptibility to, 1 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 0.285 (Asian), derived from 1000 genomes (2012-04-30). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.3
DANN	Benign	0.71

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: rs2070833; hg19: chr17-41242849; COSMIC: COSV58803303; COSMIC: COSV58803303;