NM_007294.4:c.536A>T

Variant names:

• chr17-43099786-T-A
• NM_007294.4:c.536A>T

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 5P and 2B. PM2 PM5 PP3 BP6_Moderate

The NM_007294.4(BRCA1):​c.536A>T​(p.Tyr179Phe) 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 Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Y179C) has been classified as Benign.

• Frequency: Genomes: not found (cov: 31)
• Consequence: BRCA1 NM_007294.4 missense
• Clinical Significance: Likely benign criteria provided, single submitter U:1 B:1
• Conservation: PhyloP100: 3.36

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 Uncertain_significance. Variant got 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr17-43099786-T-C is described in Lovd as [Pathogenic].
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.749
• BP6: Variant 17-43099786-T-A is Benign according to our data. Variant chr17-43099786-T-A is described in ClinVar as [Likely_benign]. Clinvar id is 1687140.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRCA1	NM_007294.4	c.536A>T	p.Tyr179Phe	missense_variant	Exon 7 of 23	ENST00000357654.9	NP_009225.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BRCA1	ENST00000357654.9	c.536A>T	p.Tyr179Phe	missense_variant	Exon 7 of 23	1	NM_007294.4	ENSP00000350283.3

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 31

ClinVar

Significance: Likely benign

Submissions summary: Uncertain:1 Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Familial cancer of breast Uncertain:1

-

Center for Precision Medicine, Meizhou People's Hospital

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: curation

- -

Hereditary breast ovarian cancer syndrome Benign:1

Feb 24, 2025

Breast Care Center, Daerim St. Mary`s Hospital

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This c.536A>T (p.Tyr179Phe) variant is a missense variant located in coding exon 7 of the BRCA1 gene. Although multiple computational prediction tools support a deleterious effect on the BRCA1 or its product, well-established functional studies have shown no damaging effect on protein function or splicing (PMID:33087888). This variant is not reported in the gnomAD genomes and exomes database. However, we identified 52 cases (2.32%) among 2,242 individuals at high risk for hereditary breast and ovarian cancer syndrome. Of these, 40 cases (2.29%) were found in affected individuals, including those with breast cancer (n = 1,673), ovarian cancer (n = 11), and other cancers such as prostate and pancreatic cancer. The remaining 12 cases (2.41%) were observed in unaffected individuals with a family history of breast and/or ovarian cancer (n = 498). In particular, eight individuals were co-detected with pathogenic variants in BRCA1 (three cases) or BRCA2 (five cases), including five individuals with breast cancer. The cis/trans status could not be determined for the BRCA1 cases. Based on the available evidence, this variant is classified as likely benign. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.15
BayesDel_addAF	Pathogenic	0.36	D
BayesDel_noAF	Pathogenic	0.28
CADD	Benign	22
DANN	Uncertain	0.98
DEOGEN2	Benign	0.14	.;T;.;.;.;.;.;T;.;T;.;T;T;.;T;T
Eigen	Uncertain	0.46
Eigen_PC	Uncertain	0.43
FATHMM_MKL	Uncertain	0.88	D
LIST_S2	Uncertain	0.91	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
M_CAP	Pathogenic	0.75	D
MetaRNN	Pathogenic	0.75	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Pathogenic	1.0	D
MutationAssessor	Uncertain	2.5	M;M;M;M;.;M;.;.;.;.;.;.;.;.;.;.
PrimateAI	Uncertain	0.59	T
PROVEAN	Benign	-0.26	N;N;N;N;N;N;N;N;N;N;N;.;N;N;N;N
REVEL	Pathogenic	0.70
Sift	Benign	0.21	T;D;D;T;D;T;D;T;T;D;D;.;D;D;D;T
Sift4G	Benign	0.64	T;T;D;T;T;T;.;.;T;.;D;.;D;.;D;.
Polyphen		0.98, 0.99, 1.0, 1.0	.;D;.;.;.;D;.;D;.;.;D;.;.;.;.;.
Vest4		0.58
MutPred		0.39		Loss of phosphorylation at Y179 (P = 0.0493);Loss of phosphorylation at Y179 (P = 0.0493);Loss of phosphorylation at Y179 (P = 0.0493);Loss of phosphorylation at Y179 (P = 0.0493);.;Loss of phosphorylation at Y179 (P = 0.0493);.;.;.;.;Loss of phosphorylation at Y179 (P = 0.0493);Loss of phosphorylation at Y179 (P = 0.0493);Loss of phosphorylation at Y179 (P = 0.0493);.;Loss of phosphorylation at Y179 (P = 0.0493);.;
MVP		0.98
MPC		0.32
ClinPred		0.93	D
GERP RS		5.2
Varity_R		0.30
gMVP		0.15

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr17-41251803;