17-43051063-C-T

Position:

• chr17-43051063-C-T

Variant summary

Our verdict is Pathogenic. Variant got 13 ACMG points: 13P and 0B. PM1 PM2 PP3 PP5_Very_Strong

The ENST00000357654.9(BRCA1):​c.5332G>A​(p.Asp1778Asn) 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. 2/3 splice prediction tools predicting alterations to normal splicing. 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. D1778A) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 31)
• Consequence: BRCA1 ENST00000357654.9 missense, splice_region
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:7 U:2 O:1
• Conservation: PhyloP100: 4.23

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 13 ACMG points.

• PM1: In a hotspot region, there are 8 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 9 benign, 17 uncertain in ENST00000357654.9
• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.815
• PP5: Variant 17-43051063-C-T is Pathogenic according to our data. Variant chr17-43051063-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 55530.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-43051063-C-T is described in Lovd as [Pathogenic]. Variant chr17-43051063-C-T is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BRCA1	NM_007294.4	c.5332G>A	p.Asp1778Asn	missense_variant, splice_region_variant	20/23	ENST00000357654.9	NP_009225.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BRCA1	ENST00000357654.9	c.5332G>A	p.Asp1778Asn	missense_variant, splice_region_variant	20/23	1	NM_007294.4	ENSP00000350283	P4

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 31

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:7 Uncertain:2 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

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

Pathogenic, criteria provided, single submitter	clinical testing	Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), c/o University of Cambridge	Oct 02, 2015	- -
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	All of Us Research Program, National Institutes of Health	Aug 16, 2023	This variant has been reported in multiple individuals with hereditary breast and ovarian cancer (PMID: 22684231, 28364669, 29446198, 30315757, 22864640, 31853058, 18285836, 35127312, 35127315). This variant is absent from large population databases, including the Genome Aggregation Database (http://gnomad.broadinstitute.org/). Functional studies suggest that the amino acid change may not have a substantial effect on the protein function (20378548, 20516115, 25748678, 30765603), but that this variant may disrupt the protein by causing alternate splicing (PMID: 25724305, 31642931, 30315757). There is some conflicting information about this variant being observed in trans with another BRCA1 variant (22684231); however, the bulk of the evidence suggests that this variant is likely pathogenic. -
Uncertain significance, no assertion criteria provided	clinical testing	Sharing Clinical Reports Project (SCRP)	Oct 22, 2010	- -

Hereditary cancer-predisposing syndrome Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Apr 24, 2023	The c.5332G>A variant (also known as p.D1778N), located in coding exon 19 of the BRCA1 gene, results from a G to A substitution at nucleotide position 5332. The amino acid change results in aspartic acid to asparagine at codon 1778, an amino acid with highly similar properties. However, this change occurs in the last base pair of coding exon 19, which makes it likely to have some effect on normal mRNA splicing. RNA assays have shown that this variant leads to skipping of exon 21 (coding exon 19) (Houdayer C et al. Hum Mutat 2012 Aug;33:1228-38; Ahlborn LB et al. Breast Cancer Res Treat. 2015 Apr;150:289-98; Minucci A et al. Clin Biochem 2019 Jan;63:54-58; Ambry internal data). This variant has been reported in the literature in multiple individuals with personal and/or family history consistent with Hereditary Breast and Ovarian Cancer syndrome (Tischkowitz M et al. Eur J Hum Genet 2008 Jul;16:820-32; Gaj P et al. Fam Cancer, 2012 Dec;11:623-8; Ryu JM et al. Breast, 2017 Jun;33:109-116; Rebbeck TR et al. Hum Mutat, 2018 05;39:593-620; Li H et al. Genet. Med., 2020 Apr;22:701-708). This alteration has been reported in trans with another BRCA1 pathogenic alteration, but the details on how phase was confirmed were not provided (Cherbal F et al. Dis Markers 2012 ;32(6):343-53.). This variant has also been shown to segregate with breast and ovarian cancer in multiple families (Ambry internal data). In silico splice site analysis for this alteration is inconclusive. Based on the majority of available evidence to date, this variant is likely to be pathogenic. -
Likely pathogenic, criteria provided, single submitter	curation	Sema4, Sema4	Nov 22, 2021	- -

Hereditary breast ovarian cancer syndrome Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Aug 28, 2022	In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. 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 alters mRNA splicing and is expected to lead to the loss of protein expression (PMID: 22505045, 25724305, 30315757). Experimental studies have shown that this missense change does not substantially affect BRCA1 protein function (PMID: 20378548, 20516115, 25748678, 30765603). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. ClinVar contains an entry for this variant (Variation ID: 55530). This variant has been observed on the opposite chromosome (in trans) from a pathogenic variant in BRCA1 in at least one individual affected with breast cancer but no reported features of Fanconi anemia (PMID: 22684231). However, the parental genotyping data supporting this observation was not provided. This missense change has been observed in individual(s) with breast and/or ovarian cancer (PMID: 18285836, 22684231, 28364669; Invitae; external communication). 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 aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 1778 of the BRCA1 protein (p.Asp1778Asn). RNA analysis indicates that this missense change induces altered splicing and may result in an absent or disrupted protein product. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jul 18, 2023	Variant summary: BRCA1 c.5332G>A (p.Asp1778Asn) results in a conservative amino acid change in the BRCT domain (IPR001357) of the encoded protein sequence. This variant alters the last conserved nucleotide of exon 20 (also referred to as exon 21 in the literature) adjacent to the intron 20 splice donor site. Three of five in-silico tools predict a benign effect of the variant on protein function. Several computational tools predict a significant impact on normal splicing: Three predict the variant weakens the canonical 5' splicing donor site. Several recent studies have reported skipping of the entire exon 20 (also called exon 21) indicated as r.5278_5332del55 (example, Houdayer_2012, Ahlborn_2015, Minucci_2019, Karam_2019, Landrith_2020). The variant was absent in 251364 control chromosomes. c.5332G>A has been reported in the literature in individuals affected with Hereditary Breast And Ovarian Cancer Syndrome or with personal or family history of hereditary cancers in settings of multi-gene panel testing or limited BRCA1/2 testing (example, Skytte_2011, Cherbal_2012, Tischkowitz_2008, Ryu_2017, Li_2020, Karam_2019, Saita_2022). Among these ascertained reports, the variant co-occurred in trans with a different pathogenic BRCA1 variant (c.798_799delTT, p.Ser267Lysfs*19) in a young breast cancer patient with a reportedly strong family history and no features of Fanconi Anemia (Cherbal_2012). The variant has also been reported to occur in cis with a different pathogenic BRCA1 variant (c.5342T>A, p.Met1775Lys) in an early onset (age 46) breast cancer patient reporting a maternal family history and an unaffected father who tested negative for both variants, thereby indicating potential in cis phasing of these variants (Tischkowitz_2008). Additional assessments on protein function for the missense change alone, report that the most pronounced variant effect results in 30%-50% of normal homology directed repair (HDR) activity (Findlay_2018) with other reports suggesting minimal to no effect on protein function (example, Lee_2010, Rowling_2010, Gaboriau_2015, Fernandes_2019). However, clinical and experimental evidence together suggest the variant is likely associated with disease based on aberrant splicing effects, not the effect of the missense change alone. The following publications have been ascertained in the context of this evaluation (PMID: 25724305, 22684231, 30765603, 30209399, 25748678, 22505045, 31642931, 32133419, 20516115, 31853058, 30315757, 29446198, 20378548, 28364669, 35127315, 21371001, 18285836). Five submitters have cited clinical-significance assessments for this variant to ClinVar after 2014, classifying the variant as pathogenic (n=1), or likely pathogenic (n=4). Based on the evidence outlined above, the variant was classified as likely pathogenic. -

not provided Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Mar 14, 2022

Observed in individuals with breast or ovarian cancer, including a co-occurrence with a pathogenic BRCA1 variant stated to be in trans however explanation of phase identification not provided (Tischkowitz 2008, Cherbal 2012, Ryu 2017); Although assays measuring the impact of the predicted protein substitution demonstrate mild or no effect on protein function (Rowling 2010, Lee 2010, Gaboriau 2015), the damaging impact is due to aberrant splicing rather than a missense substitution; Not observed at significant frequency in large population cohorts (gnomAD); Also known as 5451G>A; In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 15235020, 28364669, 30209399, 30315757, 30765603, 31131967, 18285836, 20378548, 17305420, 15172985, 25748678, 24569164, 22505045, 22245140, 25724305, 29446198, 31642931, 32133419, 20516115, 22684231, 35127315, 35127312, 33875706, 31853058) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Uncertain	0.092	D
BayesDel_noAF	Benign	-0.11
CADD	Pathogenic	33
DANN	Pathogenic	1.0
DEOGEN2	Benign	0.14	.;T;.;T;T;.;.
Eigen	Pathogenic	0.73
Eigen_PC	Pathogenic	0.71
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Uncertain	0.86	D;D;D;D;D;D;D
M_CAP	Pathogenic	0.62	D
MetaRNN	Pathogenic	0.82	D;D;D;D;D;D;D
MetaSVM	Uncertain	0.67	D
MutationAssessor	Uncertain	2.1	.;M;.;.;.;.;.
MutationTaster	Benign	1.0	D;D;D;D;D;D;D;D;D;D;D;D;N;N
PrimateAI	Benign	0.41	T
PROVEAN	Uncertain	-3.6	D;N;.;.;.;N;D
REVEL	Uncertain	0.58
Sift	Benign	0.057	T;D;.;.;.;D;D
Sift4G	Benign	0.13	T;D;D;T;T;D;T
Polyphen		0.041, 0.96	.;B;.;.;D;.;.
Vest4		0.51
MVP		0.86
MPC		0.25
ClinPred		0.97	D
GERP RS		5.2
Varity_R		0.59
gMVP		0.35

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.98
SpliceAI score (max)		0.12		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: rs80357112; hg19: chr17-41203080;