17-43070950-G-A

Position:

• chr17-43070950-G-A

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM1 PM2 PM5 PP3_Moderate PP5_Very_Strong

The ENST00000357654.9(BRCA1):​c.4964C>T​(p.Ser1655Phe) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S1655A) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: BRCA1 ENST00000357654.9 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:11 U:1 O:1
• Conservation: PhyloP100: 5.40

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 16 ACMG points.

• PM1: In a hotspot region, there are 4 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 7 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 chr17-43070951-A-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 373826.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=1, Pathogenic=2, Uncertain_significance=2, not_provided=1}.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.868
• PP5: Variant 17-43070950-G-A is Pathogenic according to our data. Variant chr17-43070950-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 55333.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-43070950-G-A is described in Lovd as [Pathogenic]. Variant chr17-43070950-G-A is described in Lovd as [Likely_pathogenic]. Variant chr17-43070950-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BRCA1	NM_007294.4	c.4964C>T	p.Ser1655Phe	missense_variant	15/23	ENST00000357654.9	NP_009225.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BRCA1	ENST00000357654.9	c.4964C>T	p.Ser1655Phe	missense_variant	15/23	1	NM_007294.4	ENSP00000350283	P4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:11 Uncertain:1 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Breast-ovarian cancer, familial, susceptibility to, 1 Pathogenic:3 Uncertain:1 Other:1

Uncertain significance, no assertion criteria provided	clinical testing	Breast Cancer Information Core (BIC) (BRCA1)	May 29, 2002	- -
not provided, no classification provided	in vitro	Brotman Baty Institute, University of Washington	-	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -
Pathogenic, criteria provided, single submitter	clinical testing	Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet	May 27, 2024	PP3; PS3; PP1_Strong; PM2_Supporting -
Pathogenic, criteria provided, single submitter	clinical testing	Human Genetics Bochum, Ruhr University Bochum	May 03, 2023	ACMG criteria used to clasify this variant:PS3, PS4, PM2_SUP, PP1 -

Hereditary breast ovarian cancer syndrome Pathogenic:4

Likely pathogenic, criteria provided, single submitter	research	Genetics Program, Instituto Nacional de Cancer	Nov 01, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 12, 2022	For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this missense change affects BRCA1 function (PMID: 15133502, 15133503, 17308087, 20516115, 23867111, 28398198). Advanced modeling performed at Invitae incorporating data from internal and/or published experimental studies (PMID: 30209399) indicates that this missense variant is expected to disrupt BRCA1 function. ClinVar contains an entry for this variant (Variation ID: 55333). This missense change has been observed in individual(s) with breast and/or ovarian cancer (PMID: 19200354, 19563646, 24249303, 27767231, 29176636). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces serine, which is neutral and polar, with phenylalanine, which is neutral and non-polar, at codon 1655 of the BRCA1 protein (p.Ser1655Phe). -
Pathogenic, criteria provided, single submitter	clinical testing	Cancer Variant Interpretation Group UK, Institute of Cancer Research, London	Oct 31, 2018	Data included in classification: The variant was observed in 2 independent UK families undergoing clinical diagnostic testing, the denominator of which dataset of clinical testing was 16,600. Case control comparison against ethnically matched population data (2/16,600 in familial cases against 0/63,369 GNOMAD NFE controls pexact= 0.04 (PS4). The variant is absent in the remainder of the GNOMAD populations (75,263 individuals) (PM2). Predicted deleterious on SIFT, Align GVGD and Polyphen HumVar (PP3). Non-functional in SGE haploid BRCA1-assay (Findlay et al. 2018), an assay well validated against ENIGMA/ClinVar (PS3) The variant is located in the BRCT1 domain (PM1_sup). c.4963T>C p.(Ser1655Pro) previously classified as pathogenic by CanVIG (July 2018) (PM5). Data not included in classification: Extensive additional functional data demonstrating variant to be deleterious: Williams et al. Carvalho et al. Lee et al., Bouwman et al (2013), Domchek et al (2013), Shakya (2011). Anantha et al (2017) elife; 6 e21350 Apr: undertook functional studies confirming reduced HR activity. Computer based algorithms predicting variant to be deleterious: Iverson (2012), Gomez-Garcia (2009) and Karchin (2007). Segregation 1 in 4 in UK family. Gomez-Garcia et al (2009) demonstrated segregation in 6/6 individuals (across 2 families) but no further details provided. There are additional reports of this variant in ClinVar (2), BIC (3) and BRCA1 LOVD (11). -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jan 21, 2021	Variant summary: BRCA1 c.4964C>T (p.Ser1655Phe) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 250710 control chromosomes. c.4964C>T has been widely reported in the literature and subsequently cited by others to co-segregate with disease in multiple individuals from families affected with Hereditary Breast And Ovarian Cancer (example, Gomez_Garcia_2009), as an isolated occurrence in a proband reporting a positive history of breast cancer (example, Cotrim_2019), and isolated reports in individuals with breast cancer (example, Inagaki-Kawata_2020). These data indicate that the variant is very likely to be associated with disease. Multiple publications report experimental evidence evaluating an impact on protein function (example, Bouwman_2020, Findlay_2018). The most pronounced variant effect results in defective homologous recombination DNA repair activity in independent measures of evaluation. Multiple clinical diagnostic laboratories and one cancer variant interpretation group have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All submitters classified the variant as pathogenic (n=1)/likely pathogenic (n=3). Some cite overlapping evidence utilized in the context of this evaluation. Based on the evidence outlined above, the variant was classified as pathogenic. -

not provided Pathogenic:2

Pathogenic, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -

Gastric cancer Pathogenic:1

Pathogenic, no assertion criteria provided

research

Laboratory for Genotyping Development, RIKEN

Jul 01, 2021

- -

Hereditary cancer-predisposing syndrome Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Aug 18, 2020

The p.S1655F variant (also known as c.4964C>T), located in coding exon 14 of the BRCA1 gene, results from a C to T substitution at nucleotide position 4964. The serine at codon 1655 is replaced by phenylalanine, an amino acid with highly dissimilar properties. This alteration has been reported in multiple individuals with personal and/or family history consistent with Hereditary Breast and Ovarian Cancer syndrome (HBOC) (Gómez García et al. Breast Cancer Res. 2009; 11(1):1-12; Mohammadi et al. BMC Cancer. 2009; 9:211; Arai M et al. J. Hum. Genet. 2018 Apr;63:447-457; Cotrim DP et al. BMC Cancer. 2019 Jan;19:4). Results from two different functional studies showed this variant results in abrogation of transcriptional activation function of the protein (Carvalho et al. Cancer Res. 2007; 67(4):1494-501; Lee MS et al. Cancer Res. 2010; 70(12):4880-90; Bouwman P et al. Cancer Discov. 2013; 3(10):1142-55). An additional functional study found that this nucleotide substitution is deleterious in a high throughput genome editing haploid cell survival assay (Findlay GM et al. Nature. 2018 10;562:217-222). Experimental results from three independent studies showed that the p.S1655 residue is part of the hydrophobic phosphopeptide binding pocket of the BRCA1 protein which mediates interactions of the BRCA1 protein with various phosphopeptides in order to perform the transactivation function of the protein (Williams RS et al. Nat Struct Mol Biol. 2004; 11(6):519-25; Shiozaki et al. Mol Cell. 2004; 4(3):405-12; Lee MS et al. Cancer Res. 2010; 70(12):4880-90). This amino acid position is highly conserved in available vertebrate species. Based on internal structural analysis, this variant is predicted to be highly destabilizing to the local structure (Ambry internal data). In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.89
BayesDel_addAF	Pathogenic	0.52	D
BayesDel_noAF	Pathogenic	0.51
CADD	Pathogenic	27
DANN	Uncertain	1.0
DEOGEN2	Benign	0.39	.;T;.;.;T;.;.;.;T;.
Eigen	Pathogenic	0.79
Eigen_PC	Pathogenic	0.72
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Uncertain	0.95	D;D;D;D;D;D;D;D;D;D
M_CAP	Pathogenic	0.81	D
MetaRNN	Pathogenic	0.87	D;D;D;D;D;D;D;D;D;D
MetaSVM	Pathogenic	0.96	D
MutationAssessor	Pathogenic	3.2	.;M;.;.;.;.;.;.;.;.
MutationTaster	Benign	1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D
PrimateAI	Uncertain	0.50	T
PROVEAN	Pathogenic	-5.1	D;N;.;D;.;N;D;D;D;D
REVEL	Pathogenic	0.82
Sift	Pathogenic	0.0	D;D;.;D;.;D;D;D;D;D
Sift4G	Pathogenic	0.0010	D;D;D;D;D;D;D;.;.;D
Polyphen		1.0, 1.0	.;D;.;.;.;.;.;.;D;.
Vest4		0.88
MVP		0.97
MPC		0.32
ClinPred		1.0	D
GERP RS		4.8
Varity_R		0.98
gMVP		0.83

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs80357390; hg19: chr17-41222967;