rs868045
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001481.3(GAS8):āc.597A>Gā(p.Glu199=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 1,611,578 control chromosomes in the GnomAD database, including 125,276 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.36 ( 10512 hom., cov: 33)
Exomes š: 0.39 ( 114764 hom. )
Consequence
GAS8
NM_001481.3 synonymous
NM_001481.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.00
Genes affected
GAS8 (HGNC:4166): (growth arrest specific 8) This gene includes 11 exons spanning 25 kb and maps to a region of chromosome 16 that is sometimes deleted in breast and prostrate cancer. The second intron contains an apparently intronless gene, C16orf3, that is transcribed in the opposite orientation. This gene is a putative tumor suppressor gene. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BP6
Variant 16-90036427-A-G is Benign according to our data. Variant chr16-90036427-A-G is described in ClinVar as [Benign]. Clinvar id is 402891.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=3 with no splicing effect.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GAS8 | NM_001481.3 | c.597A>G | p.Glu199= | synonymous_variant | 6/11 | ENST00000268699.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GAS8 | ENST00000268699.9 | c.597A>G | p.Glu199= | synonymous_variant | 6/11 | 1 | NM_001481.3 | P4 |
Frequencies
GnomAD3 genomes AF: 0.360 AC: 54756AN: 152016Hom.: 10501 Cov.: 33
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GnomAD3 exomes AF: 0.320 AC: 80201AN: 250594Hom.: 14763 AF XY: 0.325 AC XY: 43984AN XY: 135434
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GnomAD4 exome AF: 0.386 AC: 563155AN: 1459444Hom.: 114764 Cov.: 43 AF XY: 0.384 AC XY: 278481AN XY: 725566
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GnomAD4 genome AF: 0.360 AC: 54803AN: 152134Hom.: 10512 Cov.: 33 AF XY: 0.350 AC XY: 26060AN XY: 74382
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Primary ciliary dyskinesia 33 Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 10, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 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: Frequency - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 11, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at