chr17-43074658-A-T

Variant names:

• chr17-43074658-A-T
• rs2236762
• NM_007294.4:c.4485-137T>A

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_007294.4(BRCA1):​c.4485-137T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 775,348 control chromosomes in the GnomAD database, including 62,443 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★★).

• Frequency:
  • Genomes: 𝑓 0.45 (17307 hom., cov: 31)
  • Exomes 𝑓: 0.37 (45136 hom.)
• Consequence: BRCA1 NM_007294.4 intron
• Clinical Significance: Benign reviewed by expert panel B:5
• Conservation: PhyloP100: -0.576
• Publications: 15 publications found

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]

BRCA1 Gene-Disease associations (from GenCC):

• breast-ovarian cancer, familial, susceptibility to, 1

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, ClinGen, Labcorp Genetics (formerly Invitae), Genomics England PanelApp
• Fanconi anemia, complementation group S

  Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, LIMITED Submitted by: G2P, Labcorp Genetics (formerly Invitae), ClinGen, Ambry Genetics
• pancreatic cancer, susceptibility to, 4

  Inheritance: AD Classification: MODERATE Submitted by: Genomics England PanelApp
• hereditary breast ovarian cancer syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• Fanconi anemia

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 17-43074658-A-T is Benign according to our data. Variant chr17-43074658-A-T is described in ClinVar as Benign. ClinVar VariationId is 209375.Status of the report is reviewed_by_expert_panel, 3 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRCA1	NM_007294.4	c.4485-137T>A		intron_variant	Intron 13 of 22	ENST00000357654.9	NP_009225.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BRCA1	ENST00000357654.9	c.4485-137T>A		intron_variant	Intron 13 of 22	1	NM_007294.4	ENSP00000350283.3

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68553 AN: 151870 Hom.: 17260 Cov.: 31

Gnomad AFR AF: 0.688

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.426

GnomAD4 exome AF: 0.370 AC: 230913 AN: 623360 Hom.: 45136 AF XY: 0.376 AC XY: 124821 AN XY: 331682

African (AFR) AF: 0.682 AC: 10996 AN: 16126

American (AMR) AF: 0.352 AC: 11211 AN: 31816

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 7140 AN: 19190

East Asian (EAS) AF: 0.351 AC: 11339 AN: 32294

South Asian (SAS) AF: 0.527 AC: 31692 AN: 60182

European-Finnish (FIN) AF: 0.395 AC: 13117 AN: 33242

Middle Eastern (MID) AF: 0.430 AC: 1070 AN: 2490

European-Non Finnish (NFE) AF: 0.333 AC: 131928 AN: 395630

Other (OTH) AF: 0.383 AC: 12420 AN: 32390

GnomAD4 genome AF: 0.452 AC: 68657 AN: 151988 Hom.: 17307 Cov.: 31 AF XY: 0.454 AC XY: 33704 AN XY: 74290

African (AFR) AF: 0.688 AC: 28544 AN: 41464

American (AMR) AF: 0.376 AC: 5743 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1264 AN: 3470

East Asian (EAS) AF: 0.370 AC: 1913 AN: 5170

South Asian (SAS) AF: 0.521 AC: 2509 AN: 4818

European-Finnish (FIN) AF: 0.404 AC: 4258 AN: 10528

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.340 AC: 23141 AN: 67968

Other (OTH) AF: 0.429 AC: 904 AN: 2108

Alfa AF: 0.400 Hom.: 1651

Bravo AF: 0.455

Asia WGS AF: 0.466 AC: 1621 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: reviewed by expert panel

Submissions by phenotype

not specified Benign:3

-

Genome Diagnostics Laboratory, University Medical Center Utrecht

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

-

Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Nov 01, 2017

GeneKor MSA

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breast-ovarian cancer, familial, susceptibility to, 1 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 0.3304 (Asian), 0.2846 (African), 0.3668 (European), derived from 1000 genomes (2012-04-30). -

not provided Benign:1

Jun 23, 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	-0.90
CADD	Benign	0.078
DANN	Benign	0.66
PhyloP100		-0.58
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2236762; hg19: chr17-41226675; COSMIC: COSV58801011;