rs80357201
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBP6_Very_Strong
The NM_007294.4(BRCA1):c.3296C>T(p.Pro1099Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000263 in 1,613,482 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 Benign (★★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P1099R) has been classified as Likely benign.
Frequency
Consequence
NM_007294.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BRCA1 | NM_007294.4 | c.3296C>T | p.Pro1099Leu | missense_variant | 10/23 | ENST00000357654.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BRCA1 | ENST00000357654.9 | c.3296C>T | p.Pro1099Leu | missense_variant | 10/23 | 1 | NM_007294.4 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000178 AC: 27AN: 152038Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000303 AC: 76AN: 250562Hom.: 0 AF XY: 0.000340 AC XY: 46AN XY: 135434
GnomAD4 exome AF: 0.000272 AC: 398AN: 1461326Hom.: 0 Cov.: 39 AF XY: 0.000292 AC XY: 212AN XY: 726948
GnomAD4 genome AF: 0.000177 AC: 27AN: 152156Hom.: 0 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74388
ClinVar
Submissions by phenotype
Breast-ovarian cancer, familial, susceptibility to, 1 Benign:10
Benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | Oct 09, 2014 | - - |
Benign, no assertion criteria provided | clinical testing | Breast Cancer Information Core (BIC) (BRCA1) | May 29, 2002 | - - |
Benign, criteria provided, single submitter | clinical testing | Genetics and Molecular Pathology, SA Pathology | Aug 23, 2021 | The BRCA1 c.3296C>T variant is classified as Benign (BS1, BP6) - |
Benign, criteria provided, single submitter | clinical testing | Counsyl | Feb 25, 2016 | - - |
Benign, no assertion criteria provided | clinical testing | BRCAlab, Lund University | Mar 02, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
Benign, reviewed by expert panel | curation | Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) | Aug 10, 2015 | IARC class based on posterior probability from multifactorial likelihood analysis, thresholds for class as per Plon et al. 2008 (PMID: 18951446). Class 1 based on posterior probability = 0.0000000000309 - |
Benign, criteria provided, single submitter | clinical testing | Michigan Medical Genetics Laboratories, University of Michigan | Nov 03, 2014 | - - |
Benign, criteria provided, single submitter | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | Sep 21, 2015 | - - |
Likely benign, criteria provided, single submitter | clinical testing | All of Us Research Program, National Institutes of Health | Dec 18, 2023 | - - |
not specified Uncertain:1Benign:4
Benign, criteria provided, single submitter | clinical testing | Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital | Aug 15, 2023 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jun 16, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Multiple papers descrive as non-pathogenic; ClinVar: 4 B/LB - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 23, 2014 | 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. - |
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute | - | - - |
not provided Benign:4
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Aug 21, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Mar 25, 2016 | Variant summary: The variant c.3296C>T affects a conserved nucleotide, leading to amino acid change from Pro to Leu. 3/4 in-silico tools predict this variant to be damaging, however they are not definite. The variant was observed in the large and broad cohorts of the ExAC project at an allele frequency of 0.0.00026 (32/122380 chromosomes), which does not exceed the maximal expected allele frequency for a pathogenic variant in BRCA1 (0.001). However, the frequency data should still suggest that this variant is likely to be a rare polymorphism. In reputable databases (BIC and UMD), the variant has been reported to co-occur with multiple deleterious pathogenic variants in BRCA1 (p.Glu1060Ter, c.2376_2376delG and c.798_799delTT) as well as in BRCA2 (c.4277delC and c.5353delA). In addition, the variant is also known to be present with a deleterious BRCA1 variant p.Glu1060Ter (Judkins_2005), a definite evidence for benign outcome. Multifactorial probability model studies also show the variant to have a very low probability of being deleterious. Multiple clinical laboratories, reputable databases, and literature classify this variant as benign/polymorphism. Taken all together, this variant has been classified as Benign. - |
Likely benign, no assertion criteria provided | clinical testing | Department of Pathology and Laboratory Medicine, Sinai Health System | - | The BRCA1 p.Pro1099Leu variant was identified in 22 of 114568 proband chromosomes (frequency: 0.0002) from individuals or families with breast or ovarian cancer (Judkins 2005, Simard 2007, Borg 2010). The variant was also identified in the following databases: dbSNP (ID: rs80357201) as "With other allele ", ClinVar (classified as benign by Invitae, Ambry Genetics, GeneDx and 7 other submitters; as likely benign by three submitters; as uncertain significance by one submitter), MutDB, LOVD 3.0 (10x), UMD-LSDB (19x as neutral), BIC Database (23x with no clinical importance), and in ARUP Laboratories (not pathogenic or of no clinical significance). In UMD the variant was identified with a co-occurring pathogenic BRCA2 variant (c.4277delC, p.Thr1426Asns*22 and c.5353delA, p.Thr1785Leufs*6), increasing the likelihood that the p.Pro1099Leu variant does not have clinical significance. The variant was not identified in COGR, Cosmic, or Zhejiang University databases. The variant was identified in control databases in 87 of 276300 chromosomes at a frequency of 0.0003 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: Other in 3 of 6452 chromosomes (freq: 0.0005), Latino in 17 of 34400 chromosomes (freq: 0.0005), European in 30 of 126188 chromosomes (freq: 0.0002), East Asian in 1 of 18866 chromosomes (freq: 0.00005), Finnish in 14 of 25458 chromosomes (freq: 0.0006), and South Asian in 22 of 30778 chromosomes (freq: 0.0007); it was not observed in the African or Ashkenazi Jewish populations. The p.Pro1099 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 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. A few cancer research articles identified this variant in trans with known deleterious mutations (917delTT and E1060X) in clinical specimens, increasing the likelihood that the p.Pro1099Leu variant does not have clinical significance (Judkins 2005, Judkins 2005, Spurdle 2008). In addition, the variant was classified as neutral with probability of being deleterious is 3.09√ó10-11 by a computational model for BRCA1 and BRCA2 variants that factored in data on segregation, co-occurrence, personal and family histories, and pathology (Lindor 2012). 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. - |
Likely benign, no assertion criteria provided | research | Biesecker Lab/Clinical Genomics Section, National Institutes of Health | Jul 13, 2012 | - - |
Hereditary cancer-predisposing syndrome Benign:4
Likely benign, criteria provided, single submitter | clinical testing | Vantari Genetics | Jan 21, 2016 | - - |
Likely benign, criteria provided, single submitter | curation | Sema4, Sema4 | Mar 31, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Feb 19, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 18, 2014 | This alteration is classified as 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. - |
Breast and/or ovarian cancer Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario | Nov 13, 2020 | - - |
Familial cancer of breast;C2676676:Breast-ovarian cancer, familial, susceptibility to, 1;C3280442:Pancreatic cancer, susceptibility to, 4;C4554406:Fanconi anemia, complementation group S Benign:1
Benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 21, 2021 | - - |
BRCA1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 27, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Hereditary breast ovarian cancer syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at