rs10484558
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_001387994.1(BAG6):āc.642A>Gā(p.Thr214=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0271 in 1,604,910 control chromosomes in the GnomAD database, including 1,326 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: š 0.052 ( 365 hom., cov: 31)
Exomes š: 0.025 ( 961 hom. )
Consequence
BAG6
NM_001387994.1 synonymous
NM_001387994.1 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.107
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 -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP7
Synonymous conserved (PhyloP=-0.107 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BAG6 | NM_001387994.1 | c.642A>G | p.Thr214= | synonymous_variant | 7/26 | ENST00000676615.2 | NP_001374923.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BAG6 | ENST00000676615.2 | c.642A>G | p.Thr214= | synonymous_variant | 7/26 | NM_001387994.1 | ENSP00000502941 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0515 AC: 7826AN: 152104Hom.: 361 Cov.: 31
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GnomAD3 exomes AF: 0.0339 AC: 8031AN: 237004Hom.: 321 AF XY: 0.0308 AC XY: 3994AN XY: 129712
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GnomAD4 exome AF: 0.0245 AC: 35625AN: 1452688Hom.: 961 Cov.: 32 AF XY: 0.0243 AC XY: 17529AN XY: 722836
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GnomAD4 genome AF: 0.0516 AC: 7849AN: 152222Hom.: 365 Cov.: 31 AF XY: 0.0496 AC XY: 3693AN XY: 74436
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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
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at