rs80357084

Variant names:

• chr17-43106514-G-A
• rs80357084
• NM_007294.4:c.154C>T
• BRCA1 p.Leu52Phe

Your query was ambiguous. Multiple possible variants found:

• chr17-43106514-G-A
• chr17-43106514-G-C
• chr17-43106514-G-T

GermlineCancer (beta)

Variant summary

Our verdict is Benign.

-7 Benign

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received -7 classification points (ACMG Germline Pathogenicity v2019). PP3BP6_Very_Strong

The NM_007294.4(BRCA1):c.154C>T (p.Leu52Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a cumulative frequency of 0.000065 (AC=104) in the gnomAD database across 1,600,984 control chromosomes, including 1 homozygote. The grpmax filtering allele frequency (95% CI) is 0.00215. In-silico predictor (REVEL) classifies this variant as likely damaging/oncogenic. Splicing prediction tools (SpliceAI) predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign/Likely Benign (★★★). Other variants at the same amino acid position have been reported in ClinVar (not pathogenic): p.L52H: unknown significance (ClinVar VariationId 867282); p.L52I: Conflicting_classifications_of_pathogenicity (ClinVar VariationId 91556); p.L52= (synonymous): Likely_benign (ClinVar VariationId 867894, 1 star); p.L52= (synonymous): unknown significance (ClinVar VariationId 867285); p.L52= (synonymous): unknown significance (ClinVar VariationId 867284); p.L52P: Uncertain_significance (ClinVar VariationId 409340, 2 stars); p.L52R: unknown significance (ClinVar VariationId 867283); p.L52V: Uncertain_significance (ClinVar VariationId 867281, 1 star) This exact variant is curated in the UniProt human variants database as Uncertain Significance; it is also listed as a COSMIC curated somatic variant.

• Frequency:
  • Genomes: 𝑓 0.000013 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000070 (1 hom.)
• Consequence: BRCA1 NM_007294.4 missense
• Clinical Significance: Benign reviewed by expert panel P:1 U:10 B:10
• Conservation: PhyloP100: 1.30
• Publications: 69 publications found

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]

BRCA1 Gene-Disease associations (from GenCC):

• BRCA1-related cancer predisposition

  Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
• breast-ovarian cancer, familial, susceptibility to, 1

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae), Ambry Genetics
• Fanconi anemia, complementation group S

  Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, LIMITED Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae), ClinGen
• pancreatic cancer, susceptibility to, 4

  Inheritance: AD Classification: MODERATE Submitted by: Genomics England PanelApp
• hereditary breast ovarian cancer syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• Fanconi anemia

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

Classification according to ACMG Germline Pathogenicity v2019

Specifications for BRCA1 are available in the ClinGen Criteria Specification Registry and recommended for reference when assigning criteria.

Classification was made for transcript:

Our verdict: Benign. The variant received -7 points.

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	PP3Computational evidence supports damaging effect		Germline meta computational scorer (REVEL/MetaRNN/BayesDel) predicts damaging effect — supporting evidence (PP3); Splicing verdict: not pathogenic.; Germline computational verdict: pathogenic (Supporting).
	BP6Reputable source reports benign		ClinVar ≥3 stars benign — very strong (BP6); ClinVar germline classification: Benign/Likely Benign, 3 star(s).

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NM_007294.4. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRCA1	NM_007294.4	MANE Select	c.154C>T	p.Leu52Phe	missense	Exon 4 of 23	NP_009225.1	P38398-1
	BRCA1	NM_001407581.1		c.154C>T	p.Leu52Phe	missense	Exon 4 of 24	NP_001394510.1	A0A2R8Y7V5
	BRCA1	NM_001407582.1		c.154C>T	p.Leu52Phe	missense	Exon 4 of 24	NP_001394511.1	A0A2R8Y7V5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRCA1	ENST00000357654.9	TSL:1 MANE Select	c.154C>T	p.Leu52Phe	missense	Exon 4 of 23	ENSP00000350283.3	P38398-1
	BRCA1	ENST00000471181.7	TSL:1	c.154C>T	p.Leu52Phe	missense	Exon 4 of 24	ENSP00000418960.2	P38398-7
	BRCA1	ENST00000470026.6	TSL:1	c.154C>T	p.Leu52Phe	missense	Exon 4 of 23	ENSP00000419274.2	P38398-1

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 6 sources Large-scale international reference populations
GnomAD3 genomes	AF: 0.0000131	AC:2	Hom:0	AN:152094	Cov:32
GnomAD2 exomes	AF: 0.0000998	AC:25	Hom:	AN:250602	Cov:
GnomAD4 exome	AF: 0.0000704	AC:102	Hom:1	AN:1448890	Cov:28
GnomAD4 genome Warning	AF: 0.0000131	AC:2	Hom:0	AN:152094	Cov:32
TOPMed (Bravo)	AF: 0.00000378	AC:	Hom:	AN:	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.0000276	AC:6	Hom:0	AN:217610	Cov:
Local & regional cohorts 6 sources Population-specific and national genomic databases
ABraOM SABE-WGS-1171	AF: 0.000427	AC:1	Hom:0	AN:2342	Cov:
ChinaMAP Phase 1	AF: 0.000443	AC:	Hom:	AN:	Cov:
GenomeAsia100K	AF: 0.000578	AC:2	Hom:	AN:3472	Cov:
Korea4K (4,157 Koreans)	AF: 0.00747	AC:54	Hom:	AN:7232	Cov:
ToMMo 61KJPN (+60KJPN MNV)	AF: 0.00329	AC:404	Hom:1	AN:122636	Cov:
WBBC (Westlake BioBank for Chinese) pilot	AF: 0.000112	AC:1	Hom:0	AN:8960	Cov:

Showing 12 sources

Case/control cohorts

Cohort	Cases			Controls
	AF	AC	AN	AF	AC	AN
Epi25(Epilepsy)	0.0000479	2	41792	0.0000150	1	66770
SCHEMA(Schizophrenia)	0.000310	32	103210	0.000212	39	184242

Showing 2 cohortsAllele count / allele number. AF is computed from the counts for ASC (not provided by the source).

ClinVar

ClinVar submissions

Significance: Benign

Revision: reviewed by expert panel

Pathogenic	VUS	Benign	Condition
-	6	-	Breast-ovarian cancer, familial, susceptibility to, 1 (6)
-	2	2	not provided (4)
-	-	3	Hereditary cancer-predisposing syndrome (3)
-	-	3	not specified (3)
-	1	1	Hereditary breast ovarian cancer syndrome (2)
-	-	1	BRCA1-related cancer predisposition (1)
-	1	-	Breast and/or ovarian cancer (1)
1	-	-	Ovarian cancer (1)

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Pathogenic	25
AlphaMissense	Pathogenic	0.60
BayesDel_addAF	Benign	-0.045	T
BayesDel_noAF	Pathogenic	0.14
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.44	T
Eigen	Uncertain	0.57
Eigen_PC	Uncertain	0.54
FATHMM_MKL	Uncertain	0.87	D
FuncVEP CTI	Benign	0.020
GPN-Star LLR	N/A	-4.9
GPN-Star score	N/A	4.9
LIST_S2	Uncertain	0.86	D
M_CAP	Pathogenic	0.62	D
MetaRNN	Benign	0.36	T
MetaSVM	Pathogenic	0.82	D
Mutation Taster	N/A	40/60	disease causing
MutationAssessor	Benign	1.2	L
PhyloP100	Benign	1.3
popEVE	Benign	-4.4
PrimateAI	Uncertain	0.58	T
PROVEAN	Benign	-1.4	N
REVEL	Pathogenic	0.68
Sift	Uncertain	0.0070	D
Sift4G	Uncertain	0.025	D
Varity_R	N/A	0.61
VESM-3B	Benign	-7.6

Showing 28 of 28 scores

Splicing Scores

Algorithm	Calibrated pred.	Score	Prediction
Pangolin (max)	Benign	0.18
Pangolin loss	Benign	0.18	Position offset: 19
SpliceAI score (max)	Benign	0.13	Details are displayed if max score is > 0.2
Splicevardb	N/A	2.0

Showing 4 of 4 scores

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs80357084;

hg19: chr17-41258531;

COSMIC: COSV58784275;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar