chr2-214781318-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM1BP6BS1BS2_Supporting
The NM_000465.4(BARD1):c.556A>G(p.Ser186Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000044 in 1,612,818 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000465.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000480 AC: 12AN: 250122Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135130
GnomAD4 exome AF: 0.0000452 AC: 66AN: 1460616Hom.: 0 Cov.: 34 AF XY: 0.0000385 AC XY: 28AN XY: 726378
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152202Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74358
ClinVar
Submissions by phenotype
Familial cancer of breast Uncertain:3
This sequence change replaces serine, which is neutral and polar, with glycine, which is neutral and non-polar, at codon 186 of the BARD1 protein (p.Ser186Gly). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individual(s) with clinical features of BARD1-related conditions (PMID: 25186627, 30982232, 31666926, 32068069, 33309985, 34754157). ClinVar contains an entry for this variant (Variation ID: 230396). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. RNA analysis performed to evaluate the impact of this missense change on mRNA splicing indicates it does not significantly alter splicing (internal data). 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. -
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Hereditary cancer-predisposing syndrome Uncertain:1Benign:2
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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. -
not specified Uncertain:2
Variant summary: BARD1 c.556A>G (p.Ser186Gly) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 4.8e-05 in 250122 control chromosomes. This frequency is not significantly higher than expected for a pathogenic variant in BARD1 causing Hereditary Breast And Ovarian Cancer Syndrome (4.8e-05 vs 0.00025). However, the variant was found in the East Asian population at a frequency that is 2.4 fold above the maximum expected allele frequency for a pathogenic variant, suggesting the variant is a benign polymorphism in the East Asian population. c.556A>G has been reported in the literature in individuals affected with breast, colorectal and biliary tract cancer as well as in patients with PJS, without strong evidence for causality (Tung_2015, Wang_2019, Terashima_2019, Kwong_2020, Fujita_2020, Gu_2021). These reports do not provide unequivocal conclusions about association of the variant with Hereditary Breast And Ovarian Cancer Syndrome. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Eight clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Seven submitters classified the variant as VUS while one classified as likely benign. Based on the evidence outlined above, the variant was classified as VUS - possibly benign. -
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not provided Uncertain:2
In silico analysis supports that this missense variant does not alter protein structure/function; In silico analysis suggests this variant may impact gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown.; Observed in individuals with breast and pancreatic cancer, but also in unaffected controls (Tung et al., 2015; Mizukami et al., 2020); This variant is associated with the following publications: (PMID: 19139070, 23056176, 25186627, 32566746, 32980694) -
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Malignant tumor of breast Uncertain:1
The BARD1 p.Ser186Gly variant was not identified in the literature nor was it identified in the Cosmic, or MutDB databases. The variant was identified in dbSNP (ID: rs16852741) as “With Uncertain significance allele”, ClinVar (as uncertain significance by Ambry Genetics, GeneDx, Color Genomics, Invitae, and Laboratory Corporation of America), Clinvitae (3x as in ClinVar), and Zhejiang Colon Cancer Database (1x). The variant was identified in control databases in 12 of 244950 chromosomes at a frequency of 0.000049 (Genome Aggregation Database Feb 27, 2017). Breakdown of the observations by population include Other in 1 of 5462 chromosomes (freq: 0.000183), East Asian in 11 of 17222 chromosomes (freq: 0.000639), while the variant was not observed in the African, Latino, European (Non-Finnish), Ashkenazi Jewish, European Finnish, and South Asian populations. The p.Ser186Gly residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The variant occurs outside of the splicing consensus sequence and 5 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing. However, this information is not predictive enough to assume pathogenicity. In addition, the variant was identified with a co-occurring pathogenic PALB2 variant (p.Arg414X), increasing the likelihood that the p.Ser186Gly variant does not have clinical significance. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance. -
Hereditary breast ovarian cancer syndrome Uncertain:1
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Ovarian cancer Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at