chr3-52406253-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PP3_ModerateBP6_Very_StrongBS1BS2
The NM_004656.4(BAP1):c.783G>A(p.Gln261=) variant causes a splice region, synonymous change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000699 in 1,614,166 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_004656.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BAP1 | NM_004656.4 | c.783G>A | p.Gln261= | splice_region_variant, synonymous_variant | 9/17 | ENST00000460680.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BAP1 | ENST00000460680.6 | c.783G>A | p.Gln261= | splice_region_variant, synonymous_variant | 9/17 | 1 | NM_004656.4 | P1 | |
BAP1 | ENST00000296288.9 | c.729G>A | p.Gln243= | splice_region_variant, synonymous_variant | 9/17 | 5 | |||
BAP1 | ENST00000471532.5 | n.950G>A | splice_region_variant, non_coding_transcript_exon_variant | 4/5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00350 AC: 533AN: 152218Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.000919 AC: 231AN: 251284Hom.: 1 AF XY: 0.000692 AC XY: 94AN XY: 135862
GnomAD4 exome AF: 0.000404 AC: 590AN: 1461830Hom.: 5 Cov.: 35 AF XY: 0.000360 AC XY: 262AN XY: 727218
GnomAD4 genome AF: 0.00354 AC: 539AN: 152336Hom.: 2 Cov.: 33 AF XY: 0.00354 AC XY: 264AN XY: 74502
ClinVar
Submissions by phenotype
not specified Benign:4
Benign, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Apr 02, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital | Aug 15, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 23, 2019 | - - |
BAP1-related tumor predisposition syndrome Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Hereditary cancer-predisposing syndrome Benign:2
Benign, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Mar 18, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 14, 2015 | 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. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 11, 2019 | This variant is associated with the following publications: (PMID: 28062663) - |
Melanoma, uveal, susceptibility to, 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | KCCC/NGS Laboratory, Kuwait Cancer Control Center | Jul 07, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at