rs111682654
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_004281.4(BAG3):c.498C>T(p.His166=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000975 in 1,609,460 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00033 ( 2 hom., cov: 33)
Exomes 𝑓: 0.000073 ( 3 hom. )
Consequence
BAG3
NM_004281.4 synonymous
NM_004281.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.70
Genes affected
BAG3 (HGNC:939): (BAG cochaperone 3) BAG proteins compete with Hip for binding to the Hsc70/Hsp70 ATPase domain and promote substrate release. All the BAG proteins have an approximately 45-amino acid BAG domain near the C terminus but differ markedly in their N-terminal regions. The protein encoded by this gene contains a WW domain in the N-terminal region and a BAG domain in the C-terminal region. The BAG domains of BAG1, BAG2, and BAG3 interact specifically with the Hsc70 ATPase domain in vitro and in mammalian cells. All 3 proteins bind with high affinity to the ATPase domain of Hsc70 and inhibit its chaperone activity in a Hip-repressible manner. [provided by RefSeq, Jul 2008]
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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=-0.6).
BP6
?
Variant 10-119670168-C-T is Benign according to our data. Variant chr10-119670168-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 389951.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-119670168-C-T is described in Lovd as [Likely_benign].
BP7
?
Synonymous conserved (PhyloP=-1.7 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000328 (50/152366) while in subpopulation AFR AF= 0.00108 (45/41584). AF 95% confidence interval is 0.000831. There are 2 homozygotes in gnomad4. There are 25 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 50 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BAG3 | NM_004281.4 | c.498C>T | p.His166= | synonymous_variant | 2/4 | ENST00000369085.8 | |
BAG3 | XM_005270287.2 | c.498C>T | p.His166= | synonymous_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BAG3 | ENST00000369085.8 | c.498C>T | p.His166= | synonymous_variant | 2/4 | 1 | NM_004281.4 | P1 | |
BAG3 | ENST00000450186.1 | c.324C>T | p.His108= | synonymous_variant | 3/5 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000269 AC: 41AN: 152248Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000876 AC: 21AN: 239668Hom.: 0 AF XY: 0.0000762 AC XY: 10AN XY: 131214
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GnomAD4 exome AF: 0.0000734 AC: 107AN: 1457094Hom.: 3 Cov.: 34 AF XY: 0.0000648 AC XY: 47AN XY: 724826
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GnomAD4 genome ? AF: 0.000328 AC: 50AN: 152366Hom.: 2 Cov.: 33 AF XY: 0.000336 AC XY: 25AN XY: 74508
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 25, 2019 | - - |
Myofibrillar myopathy 6;C3151293:Dilated cardiomyopathy 1HH Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 05, 2019 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
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Name
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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