chr6-31644000-T-C
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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.1669-23A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.825 in 1,613,678 control chromosomes in the GnomAD database, including 550,293 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 0.81 ( 49963 hom., cov: 31)
Exomes 𝑓: 0.83 ( 500330 hom. )
Consequence
BAG6
NM_001387994.1 intron
NM_001387994.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.80
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=-0.84).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BAG6 | NM_001387994.1 | c.1669-23A>G | intron_variant | ENST00000676615.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BAG6 | ENST00000676615.2 | c.1669-23A>G | intron_variant | NM_001387994.1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.809 AC: 122901AN: 151980Hom.: 49908 Cov.: 31
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GnomAD3 exomes AF: 0.838 AC: 209298AN: 249740Hom.: 88064 AF XY: 0.837 AC XY: 113246AN XY: 135242
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GnomAD4 exome AF: 0.826 AC: 1207749AN: 1461580Hom.: 500330 Cov.: 47 AF XY: 0.827 AC XY: 601090AN XY: 727116
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GnomAD4 genome AF: 0.809 AC: 123013AN: 152098Hom.: 49963 Cov.: 31 AF XY: 0.810 AC XY: 60250AN XY: 74346
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at