6-31641339-C-T
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_001387994.1(BAG6):c.2643G>A(p.Ala881=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000456 in 1,614,210 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00056 ( 2 hom., cov: 32)
Exomes 𝑓: 0.00045 ( 0 hom. )
Consequence
BAG6
NM_001387994.1 synonymous
NM_001387994.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.530
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 -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.32).
BP6
Variant 6-31641339-C-T is Benign according to our data. Variant chr6-31641339-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 722584.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.53 with no splicing effect.
BS2
High AC in GnomAd4 at 85 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BAG6 | NM_001387994.1 | c.2643G>A | p.Ala881= | synonymous_variant | 19/26 | ENST00000676615.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BAG6 | ENST00000676615.2 | c.2643G>A | p.Ala881= | synonymous_variant | 19/26 | NM_001387994.1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000558 AC: 85AN: 152244Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.000434 AC: 109AN: 251380Hom.: 0 AF XY: 0.000397 AC XY: 54AN XY: 135870
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GnomAD4 exome AF: 0.000445 AC: 651AN: 1461848Hom.: 0 Cov.: 35 AF XY: 0.000429 AC XY: 312AN XY: 727222
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GnomAD4 genome AF: 0.000558 AC: 85AN: 152362Hom.: 2 Cov.: 32 AF XY: 0.000564 AC XY: 42AN XY: 74516
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 25, 2018 | - - |
Computational scores
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Benign
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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