chr13-32379912-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4_ModerateBP6
The NM_000059.4(BRCA2):c.9116C>T(p.Pro3039Leu) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000614 in 1,613,014 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. P3039P) has been classified as Pathogenic.
Frequency
Consequence
NM_000059.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| BRCA2 | ENST00000380152.8 | c.9116C>T | p.Pro3039Leu | missense_variant, splice_region_variant | Exon 23 of 27 | 5 | NM_000059.4 | ENSP00000369497.3 | ||
| BRCA2 | ENST00000530893.7 | c.8747C>T | p.Pro2916Leu | missense_variant, splice_region_variant | Exon 23 of 27 | 1 | ENSP00000499438.2 | |||
| BRCA2 | ENST00000614259.2 | n.*1174C>T | splice_region_variant, non_coding_transcript_exon_variant | Exon 22 of 26 | 2 | ENSP00000506251.1 | ||||
| BRCA2 | ENST00000614259 | n.*1174C>T | 3_prime_UTR_variant | Exon 22 of 25 | 2 | ENSP00000506251.1 |
Frequencies
GnomAD3 genomes 0.0000526 AC: 8AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000886 AC: 22AN: 248254Hom.: 0 AF XY: 0.0000744 AC XY: 10AN XY: 134368
GnomAD4 exome AF: 0.0000623 AC: 91AN: 1460846Hom.: 0 Cov.: 32 AF XY: 0.0000661 AC XY: 48AN XY: 726676
GnomAD4 genome 0.0000526 AC: 8AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74344
ClinVar
Submissions by phenotype
Breast-ovarian cancer, familial, susceptibility to, 2 Uncertain:3Benign:3
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The following ACMG criteria was used: BS1_SUP; BP5_Strong; BS3_Strong -
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not provided Uncertain:3Benign:2
BRCA2: BP4, BS3:Supporting -
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The BRCA2 c.9116C>T; p.Pro3039Leu variant (rs80359167) is reported in the literature in individuals affected with breast and ovarian cancer, but without clear association with disease (Azzollini 2016, Jarhelle 2017, Park 2017). This variant is also reported in ClinVar (Variation ID: 52753), and is found in the general population with an overall allele frequency of 0.0089% (22/248254 alleles) in the Genome Aggregation Database. The proline at codon 3039 is moderately conserved, and computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.349). In vitro assays show a neutral effect on homology directed repair activity (Guidugli 2018). Other computational analyses (Alamut v.2.11) predict that this variant may impact splicing by weakening the nearby canonical donor splice site, but in vitro functional studies show no effect on splicing (Colombo 2013, Menendez 2012). However, given the lack of clear clinical data, the clinical significance of the p.Pro3039Leu variant is uncertain at this time. References: Azzollini et al. Mutation detection rates associated with specific selection criteria for BRCA1/2 testing in 1854 high-risk families: A monocentric Italian study. Eur J Intern Med. 2016 Jul;32:65-71. Colombo M et al. Comparative in vitro and in silico analyses of variants in splicing regions of BRCA1 and BRCA2 genes and characterization of novel pathogenic mutations. PLoS One. 2013;8(2):e57173. Guidugli L et al. Assessment of the Clinical Relevance of BRCA2 Missense Variants by Functional and Computational Approaches. Am J Hum Genet. 2018 Feb 1;102(2):233-248. Jarhelle E et al. Characterization of BRCA1 and BRCA2 variants found in a Norwegian breast or ovarian cancer cohort. Fam Cancer. 2017 Jan;16(1):1-16. Menendez M et al. Assessing the RNA effect of 26 DNA variants in the BRCA1 and BRCA2 genes. Breast Cancer Res Treat. 2012 Apr;132(3):979-92. Park et al. Identification of a Novel BRCA1 Pathogenic Mutation in Korean Patients Following Reclassification of BRCA1 and BRCA2 Variants According to the ACMG Standards and Guidelines Using Relevant Ethnic Controls. Cancer Res Treat. 2017 Oct;49(4):1012-1021. -
Hereditary cancer-predisposing syndrome Benign:4
BS1_Supporting, BS3, BP4, BP5_Moderate c.9116C>T, located in exon 23 of the BRCA2 gene, is predicted to result in the substitution of Pro by Leu at codon 3039, p.(Pro3039Leu). It was found in 6/30496 alleles, with a filter allele frequency of 0.0085% at 95% confidence, within the South Asian population in the gnomAD v2.1 (non-cancer, exome only subset) (BS1_Supporting). This position is located in a (potentially) clinically important functional domain. SpliceAI algorithm predicts no significant impact on splicing and the Bayesdel no-AF meta-predictor score for this variant (-0.141) suggests that it does not affect the protein function (BP4). It has been reported by two calibrated studies to affect protein function similar to benign control variants (PMIDs: 33609447, 29884841) (BS3). RNA studies indicate that this variant has no effect on mRNA splicing (r.9116c>u) (PMID: 23451180, 21735045). Published clinical data for a multifactorial likelihood analysis (PMID: 31131967) showed a combined LR=0,17 (BP5_Moderate). This variant has been reported in ClinVar (3x benign, 10x likely benign, 7x uncertain significance) and LOVD (4x likely benign, 11x uncertain significance) databases, and in BRCA Exchange database as Not Yet Reviwed. Based on currently available information, the variant c.9116C>T should be considered a benign variant. -
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
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Hereditary breast ovarian cancer syndrome Uncertain:1Benign:2
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not specified Benign:3
Variant summary: BRCA2 c.9116C>T (p.Pro3039Leu) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. 4/4 computational tools predict no significant impact on normal splicing. Functional studies confirm these predictions indicating this variant has no effect on mRNA splicing (e.g. Caux-Moncoutier_2009, Houdayer_2012, Menendez_2012, Colombo_2013). The variant allele was found at a frequency of 8.9e-05 in 248254 control chromosomes (gnomAD). This frequency is not higher than estimated for a pathogenic variant in BRCA2 causing Hereditary Breast And Ovarian Cancer Syndrome (8.9e-05 vs 0.00075), allowing no conclusion about variant significance. c.9116C>T has been reported in the literature in individuals affected with Hereditary Breast And Ovarian Cancer Syndrome (example, Coulet_2010, Azzollini_2016, Rodriguez-Balada_2016, Park_2017, Guo_2020) but it was also reported in controls (Guo_2020). These reports do not provide unequivocal conclusions about association of the variant with Hereditary Breast And Ovarian Cancer Syndrome. Co-occurrences with BRCA2 pathogenic variants have been observed at our laboratory and in the literature (BRCA2 c.658_659delGT, p.Val220IlefsX4 at our laboratory; BRCA2 c.2808_2811delACAA, p.Ala938ProfsX21 in Santonocito_2020), providing supporting evidence for a benign role. Experimental evidence evaluating an impact on protein function through utilization of a homologous recombination DNA-repair activity assay, determined the variant to be neutral (example, Guidugli_2018, Hart_2019, Richardson_2021). HDR assays qualify as a recognized gold standard on the basis of updated guidance provided by the ClinGen Sequence Variant Interpretation (SVI) working group. This working group has recommended strong functional evidence (ACMG BS3) as sufficient weightage for categorization as likely benign (Tavtigian_2018). Multiple ClinVar submitters (evaluation after 2014) cite the variant with a predominant consensus as as benign/likely benign and three ClinVar submitters (evaluation after 2014) cite it as uncertain significance. Based on the evidence outlined above, the variant was classified as benign. -
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Malignant tumor of breast Benign:1
The BRCA2 p.Pro3039Leu variant was identified in 8 of 6754 proband chromosomes (frequency: 0.001) from individuals or families with hereditary breast and ovarian cancer and was not identified in 1586 control chromosomes from healthy individuals (Park 2017, Azzollini 2016, Rodriguez-Balada 2016, Jarhelle 2016, Llort 2002). The variant was identified in dbSNP (rs80359167) as “with likely benign, uncertain significance allele”, ClinVar (classified as likely benign by Invitae, GeneDx, Ambry Genetics and 7 other submitters, uncertain significance by BIC and 1 other submitter and benign by Color), LOVD 3.0 (observed 9x) and UMD-LSDB (observed 19x). The variant was identified in control databases in 22 of 248,254 chromosomes at a frequency of 0.00009 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: South Asian in 6 of 30,496 chromosomes (freq: 0.0002), Latino in 6 of 34,364 chromosomes (freq: 0.0002), African in 2 of 16,040 chromosomes (freq: 0.0001), European in 8 of 111,594 chromosomes (freq: 0.00007); it was not observed in the Ashkenazi Jewish, East Asian, Finnish, and Other populations. The variant was observed in UMD-LSDB in a sample with a co-occurring BRCA1 pathogenic variant (c.670+1G>T). In cDNA amplification assays, the variant had no observed effect on in vitro splicing (Rodriguez-Balada 2016, Colombo 2012, Houdayer 2012, Menedez 2012). The p.Pro3039 residue is conserved in mammals but not in more distantly related organisms, and four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the variant may impact the protein; however, this information is not predictive enough to assume pathogenicity. The p.Pro3039Leu variant occurs in the first base of the exon. This position has been shown to be part of the splicing consensus sequence and variants involving this position sometimes affect splicing. In addition, 1 of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predict a greater than 10% difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at