17-43106456-C-T

Position:

• chr17-43106456-C-T

Variant summary

Our verdict is Pathogenic. Variant got 15 ACMG points: 15P and 0B. PM1 PM2 PM5 PP3 PP5_Very_Strong

The ENST00000357654.9(BRCA1):​c.212G>A​(p.Arg71Lys) variant causes a missense, splice region change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R71G) has been classified as Pathogenic.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: BRCA1 ENST00000357654.9 missense, splice_region
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:10 O:1
• Conservation: PhyloP100: 4.11

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 Pathogenic. Variant got 15 ACMG points.

• PM1: In a hotspot region, there are 4 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 11 benign, 17 uncertain in ENST00000357654.9
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr17-43106457-T-C is described in ClinVar as [Pathogenic]. Clinvar id is 17693.Status of the report is reviewed_by_expert_panel, 3 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.82
• PP5: Variant 17-43106456-C-T is Pathogenic according to our data. Variant chr17-43106456-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 54471.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-43106456-C-T is described in Lovd as [Pathogenic]. Variant chr17-43106456-C-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BRCA1	NM_007294.4	c.212G>A	p.Arg71Lys	missense_variant, splice_region_variant	4/23	ENST00000357654.9	NP_009225.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BRCA1	ENST00000357654.9	c.212G>A	p.Arg71Lys	missense_variant, splice_region_variant	4/23	1	NM_007294.4	ENSP00000350283	P4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1427556 Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0 AN XY: 711784

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:10 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:3

Pathogenic, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The BRCA1 p.Arg71Lys variant was identified in 3 of 1982 proband chromosomes (frequency: 0.002) from individuals or families with breast cancer, and was not identified in 406 control chromosomes from healthy individuals (Meindl 2002, Zhang 2011). The variant was also identified in dbSNP (ID:80356913) “With untested allele”, HGMD, UMD (1X as a causal variant), and the BIC database (2X with clinical importance). The p.Arg71 residue is conserved across mammals and lower organisms; however, computational analyses (SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein and this information is not very predictive of pathogenicity. The p.Arg71Lys variant occurs in the last base of the exon. This position has been shown to be part of the splicing consensus sequence and variants involving this position sometimes affect splicing. In addition, in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing in all 5 programs. In addition, three studies demonstrated an increase in the levels of a BRCA1 mRNA isoform that had an out-of-frame deletion of the last 22 base pairs from exon 5, indicating that the variant causes aberrant splicing of the mRNA transcript (Caleca 2014, Colombo 2013, Zhang 2011). Furthermore, analysis of a tumour specimen with the variant indicated loss of heterozygosity (Zhang 2011). In summary, based on the above information, this variant meets our laboratory’s criteria to be classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	May 24, 2021	This variant has been reported in multiple individuals affected with breast/ovarian cancer in the published literature (PMID: 11802209 (2002), 31825140 (2019)). This variant was observed to cause a major splicing defect that reduces the full-length transcript to a level below the aberrant transcript (PMID: 21863257 (2011), 22505045 (2012), 23451180 (2013)). This variant has not been reported in large, multi-ethnic general populations. Variant is located in potentially critical domain of the protein. Variant is predicted to negatively affect a known splice site. Based on the available information, this variant is classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Apr 02, 2022	- -

Breast-ovarian cancer, familial, susceptibility to, 1 Pathogenic:2 Other:1

not provided, no classification provided	in vitro	Brotman Baty Institute, University of Washington	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), c/o University of Cambridge	Oct 02, 2015	- -
Pathogenic, no assertion criteria provided	clinical testing	Breast Cancer Information Core (BIC) (BRCA1)	Nov 28, 2000	- -

Hereditary cancer-predisposing syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Nov 12, 2021	The c.212G>A pathogenic mutation (also known as p.R71K and 331G>A), located in coding exon 3 of the BRCA1 gene, results from a G to A substitution at nucleotide position 212. The arginine at codon 71 is replaced by lysine, an amino acid with highly similar properties. However, this change occurs in the last base pair of coding exon 3, which makes it likely to have some effect on normal mRNA splicing. This alteration has been demonstrated to lead to the generation of an alternately spliced transcript (Zhang L et al. Breast Cancer Res Treat. 2011;130(3):1051-6; Houdayer C et al. Hum Mutat. 2012 Aug;33:1228-38). In two independent studies, using semi-quantitative and qualitative RT-PCR analysis, this alteration was shown to significantly increase the expression of delta exon 5q isoform compared to the full-length transcript (Caleca L et al. PLoS One. 2014; 6;9(2):e86924; Colombo M et al PLoS One. 2013;8(2):e57173). One functional study found that this nucleotide substitution is non-functional in a high-throughput, genome editing, haploid cell survival assay (Findlay GM et al. Nature. 2018 10;562:217-222). This alteration has also been identified in cohorts of breast and ovarian cancer patients (Meindl A et al. Int J Cancer. 2002; 1;97(4):472-80; Fang M et al. Oncol Lett. 2018 Mar;15:3068-3074; Li A et al. Gynecol Oncol. 2018 10;151:145-152). Additionally, two other pathogenic alterations, c.212G>T and c.212G>C, have been described at the same codon (Findlay GM et al. Nature. 2018 10;562:217-222; Ambry internal data). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. Based on the available evidence to date, this alteration is classified as a pathogenic mutation. -
Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Feb 25, 2021	This variant alters the conserved c.G at the last nucleotide position of exon 4 of the BRCA1 gene. This variant is also known as 331G>A in exon 5 according to the BIC nomenclature and exon naming system. This variant is predicted to disrupt mRNA splicing by computational tools. An RT-PCR analysis of RNA from a carrier individual has shown this variant to cause an in-frame skipping of exon 4 that encodes a functionally important RING domain, as well as a out-of-frame deletion of 22 nucleotides from the 3' end of exon 4, resulting in 50% decrease in normal transcripts in the carrier's cells (PMID: 21863257). This variant has also been shown to cause loss of BRCA1 function in saturation genome editing and haploid cell proliferation assay in human cells (PMID: 30209399). This variant has been reported in individuals affected with hereditary breast and ovarian cancer (PMID: 11802209, 12938098, 29435039), early-onset breast cancer (PMID 21863257), and triple-negative breast cancer (PMID: 25480878, 26577449). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Different nucleotide substitutions at the same position, c.212G>C and c.212G>T, are also thought to be disease-causing (ClinVar variation ID: 267512 and 185705). Loss of BRCA1 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic. -

Hereditary breast ovarian cancer syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Aug 28, 2023	For these reasons, this variant has been classified as Pathogenic. This sequence change replaces arginine, which is basic and polar, with lysine, which is basic and polar, at codon 71 of the BRCA1 protein (p.Arg71Lys). RNA analysis indicates that this missense change induces altered splicing and may result in an absent or disrupted protein product. This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with breast and/or ovarian cancer (PMID: 11802209, 25480878, 28724667, 29435039, 29752822). This variant is also known as 331G>A. ClinVar contains an entry for this variant (Variation ID: 54471). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this missense change results in activation of a cryptic splice site and introduces a premature termination codon (PMID: 21863257, 22505045, 23451180). The resulting mRNA is expected to undergo nonsense-mediated decay. -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Oct 17, 2022	Variant summary: BRCA1 c.212G>A (p.Arg71Lys) results in a conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. Several computational tools predict a significant impact on normal splicing: Three predict the variant abolishes a canonical 5' splicing donor site and one predicts the variant weakens the 5' donor site. At least two publications report experimental evidence that this variant completely abolishes normal mRNA splicing and instead uses a cryptic splice site 22 nucleotides upstream from the canonical 5' splice site (e.g. Zhang_2011, Houdayer_2012). The variant was absent in 249744 control chromosomes (gnomAD). c.212G>A has been reported in the literature in multiple individuals affected with breast/ovarian cancer, including those with a positive family history of these and other cancers (e.g. Meindl_2002, Zhang_2011, Francies_2015, Li_2018). These data indicate that the variant is very likely to be associated with disease. At least one functional study reports experimental evidence evaluating an impact on protein function and showed no damaging effect of this variant on homology directed repair (HDR) activity (e.g. Findlay_2018). HDR assays qualify as a recognized gold standard on the basis of updated guidance provided by the ClinGen Sequence Variant Interpretation (SVI) working group. Four submitters have provided clinical-significance assessments for this variant to ClinVar after 2014 and all classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Breast-ovarian cancer, familial, susceptibility to, 1;C3280442:Pancreatic cancer, susceptibility to, 4;C4554406:Fanconi anemia, complementation group S Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Juno Genomics, Hangzhou Juno Genomics, Inc

-

PM2_Supporting+PS3+PS4+PM5 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.68
BayesDel_addAF	Pathogenic	0.41	D
BayesDel_noAF	Pathogenic	0.35
CADD	Pathogenic	32
DANN	Uncertain	1.0
DEOGEN2	Benign	0.30	.;T;.;.;.;.;T;.;.;T;T;T;T;.
Eigen	Uncertain	0.59
Eigen_PC	Uncertain	0.57
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Benign	0.67	T;T;T;T;T;T;T;T;T;T;T;T;T;T
M_CAP	Pathogenic	0.51	D
MetaRNN	Pathogenic	0.82	D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Uncertain	0.78	D
MutationAssessor	Uncertain	2.5	M;M;M;M;.;M;.;.;.;.;.;.;.;.
MutationTaster	Benign	1.0	D;D;D;D;D;D;D;D;D;N;N;N;N;N
PrimateAI	Uncertain	0.61	T
PROVEAN	Benign	-0.75	N;N;N;N;N;N;N;N;N;.;N;N;D;.
REVEL	Pathogenic	0.74
Sift	Pathogenic	0.0	D;D;D;D;D;D;D;D;D;.;D;D;D;.
Sift4G	Benign	0.23	T;D;D;T;D;T;.;T;D;.;D;D;.;.
Polyphen		0.90, 0.98, 0.97	.;P;.;.;.;D;.;.;D;.;.;.;.;.
Vest4		0.67
MutPred		0.73		Gain of methylation at R71 (P = 0.0062);Gain of methylation at R71 (P = 0.0062);Gain of methylation at R71 (P = 0.0062);Gain of methylation at R71 (P = 0.0062);.;Gain of methylation at R71 (P = 0.0062);Gain of methylation at R71 (P = 0.0062);.;Gain of methylation at R71 (P = 0.0062);Gain of methylation at R71 (P = 0.0062);Gain of methylation at R71 (P = 0.0062);Gain of methylation at R71 (P = 0.0062);Gain of methylation at R71 (P = 0.0062);.;
MVP		0.97
MPC		0.16
ClinPred		0.96	D
GERP RS		4.6
Varity_R		0.81
gMVP		0.48

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	1.0
SpliceAI score (max)		0.65		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.65		Position offset: 0

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs80356913; hg19: chr17-41258473; COSMIC: COSV58802615; COSMIC: COSV58802615;