17-43124031-T-G

Variant summary

Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM1 PM2 PM5 PP3_Moderate

The NM_007294.4(BRCA1):c.66A>C(p.Leu22Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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 Uncertain significance (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L22S) has been classified as Pathogenic.

• Frequency: Genomes: not found (cov: 32)
• Consequence: BRCA1 NM_007294.4 missense
• Clinical Significance: Uncertain significance criteria provided, multiple submitters, no conflicts U:3 O:1
• Conservation: PhyloP100: -0.118

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 Likely_pathogenic. Variant got 8 ACMG points.

• PM1: In a hotspot region, there are 6 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 4 benign, 17 uncertain in NM_007294.4
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr17-43124032-A-G is described in ClinVar as [Pathogenic]. Clinvar id is 55656.Status of the report is reviewed_by_expert_panel, 3 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.863

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRCA1	NM_007294.4	c.66A>C	p.Leu22Phe	missense_variant	2/23	ENST00000357654.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRCA1	ENST00000357654.9	c.66A>C	p.Leu22Phe	missense_variant	2/23	1	NM_007294.4	P4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:3 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hereditary cancer-predisposing syndrome Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Jul 31, 2014

The p.L22F variant (also known as c.66A>C or 185A>C), located in coding exon 1 of the BRCA1 gene, results from an A to C substitution at nucleotide position 66. The leucine at codon 22 is replaced by phenylalanine, an amino acid with highly similar properties. This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP), and 1000 Genomes Project. In the ESP, this variant was not observed in 6502 samples (13004 alleles) with coverage at this position. To date, this alteration has been detected with an allele frequency of approximately 0.002% (greater than 64000 alleles tested) in our clinical cohort. Based on protein sequence alignment, this amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be possibly damaging and deleterious by PolyPhen and SIFT in silico analyses, respectively. Since supporting evidence is limited at this time, the clinical significance of p.L22F remains unclear. -

BRCA1-related disorder Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Jun 09, 2023

The BRCA1 c.66A>C variant is predicted to result in the amino acid substitution p.Leu22Phe. To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. In vitro studies suggested that this variant does not alter protein function (Clark et al. 2022. PubMed: 35659930). This variant is interpreted as a variant of unknown clinical significance in Clinvar (https://www.ncbi.nlm.nih.gov/clinvar/variation/185882/). A different missense variant affecting this amino acid has been classified as pathogenic by the ENIGMA expert panel (p.Leu22Ser, https://www.ncbi.nlm.nih.gov/clinvar/variation/55656/). At this time, the clinical significance of the p.Leu22Phe variant is uncertain due to the absence of conclusive functional and genetic evidence. -

Hereditary breast ovarian cancer syndrome Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Invitae

Feb 25, 2021

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant disrupts the p.Leu22 amino acid residue in BRCA1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 21990134, 25823446, 30209399, 9609997, 19543972). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt BRCA1 protein function. This variant has not been reported in the literature in individuals with BRCA1-related conditions. ClinVar contains an entry for this variant (Variation ID: 185882). This variant is not present in population databases (ExAC no frequency). This sequence change replaces leucine with phenylalanine at codon 22 of the BRCA1 protein (p.Leu22Phe). The leucine residue is highly conserved and there is a small physicochemical difference between leucine and phenylalanine. -

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

not provided, no classification provided

in vitro

Brotman Baty Institute, University of Washington

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.83
BayesDel_addAF	Pathogenic	0.28	D
BayesDel_noAF	Pathogenic	0.17
Cadd	Benign	21
Dann	Uncertain	1.0
Eigen	Benign	0.033
Eigen_PC	Benign	-0.051
FATHMM_MKL	Benign	0.54	D
LIST_S2	Uncertain	0.95	D;D;D;D;D;D;D;D;D;D;D;D;D;D
M_CAP	Pathogenic	0.65	D
MetaRNN	Pathogenic	0.86	D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Uncertain	0.0024	D
MutationAssessor	Benign	0.59	N;N;N;N;N;.;.;.;.;.;.;.;.;.
MutationTaster	Benign	0.92	D;D;D;D;D;D;D;D;N;N;N;N;N;N
PrimateAI	Uncertain	0.67	T
PROVEAN	Benign	-0.050	N;N;N;N;N;N;N;.;N;N;N;D;D;.
REVEL	Pathogenic	0.65
Sift	Uncertain	0.0030	D;D;D;D;D;D;D;.;D;D;D;D;D;.
Sift4G	Uncertain	0.023	D;D;D;T;T;.;D;.;D;.;D;.;.;.
Polyphen		1.0, 0.90, 1.0	.;D;.;.;P;.;D;.;.;.;.;.;.;.
Vest4		0.67
MutPred		0.79		Gain of ubiquitination at K20 (P = 0.0931);Gain of ubiquitination at K20 (P = 0.0931);Gain of ubiquitination at K20 (P = 0.0931);Gain of ubiquitination at K20 (P = 0.0931);Gain of ubiquitination at K20 (P = 0.0931);Gain of ubiquitination at K20 (P = 0.0931);Gain of ubiquitination at K20 (P = 0.0931);Gain of ubiquitination at K20 (P = 0.0931);Gain of ubiquitination at K20 (P = 0.0931);Gain of ubiquitination at K20 (P = 0.0931);Gain of ubiquitination at K20 (P = 0.0931);Gain of ubiquitination at K20 (P = 0.0931);Gain of ubiquitination at K20 (P = 0.0931);Gain of ubiquitination at K20 (P = 0.0931);
MVP		0.93
MPC		0.46
ClinPred		0.72	D
GERP RS		0.24
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.60
gMVP		0.59

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: rs786202533; hg19: chr17-41276048;