rs805303
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001387994.1(BAG6):c.552+88C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 1,298,384 control chromosomes in the GnomAD database, including 100,027 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.44 ( 15683 hom., cov: 31)
Exomes 𝑓: 0.38 ( 84344 hom. )
Consequence
BAG6
NM_001387994.1 intron
NM_001387994.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.224
Genes affected
BAG6 (HGNC:13919): (BAG cochaperone 6) This gene was first characterized as part of a cluster of genes located within the human major histocompatibility complex class III region. This gene encodes a nuclear protein that is cleaved by caspase 3 and is implicated in the control of apoptosis. In addition, the protein forms a complex with E1A binding protein p300 and is required for the acetylation of p53 in response to DNA damage. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BAG6 | NM_001387994.1 | c.552+88C>T | intron_variant | ENST00000676615.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BAG6 | ENST00000676615.2 | c.552+88C>T | intron_variant | NM_001387994.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.444 AC: 67418AN: 151802Hom.: 15668 Cov.: 31
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GnomAD4 exome AF: 0.378 AC: 433619AN: 1146464Hom.: 84344 AF XY: 0.372 AC XY: 214941AN XY: 578074
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GnomAD4 genome ? AF: 0.444 AC: 67474AN: 151920Hom.: 15683 Cov.: 31 AF XY: 0.446 AC XY: 33116AN XY: 74250
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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