rs706115
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004323.6(BAG1):c.*1612G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 151,874 control chromosomes in the GnomAD database, including 3,093 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 0.19 ( 3093 hom., cov: 30)
Exomes 𝑓: 0.25 ( 0 hom. )
Consequence
BAG1
NM_004323.6 3_prime_UTR
NM_004323.6 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.09
Genes affected
BAG1 (HGNC:937): (BAG cochaperone 1) The oncogene BCL2 is a membrane protein that blocks a step in a pathway leading to apoptosis or programmed cell death. The protein encoded by this gene binds to BCL2 and is referred to as BCL2-associated athanogene. It enhances the anti-apoptotic effects of BCL2 and represents a link between growth factor receptors and anti-apoptotic mechanisms. Multiple protein isoforms are encoded by this mRNA through the use of a non-AUG (CUG) initiation codon, and three alternative downstream AUG initiation codons. A related pseudogene has been defined on chromosome X. [provided by RefSeq, Feb 2010]
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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=-0.8).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BAG1 | NM_004323.6 | c.*1612G>C | 3_prime_UTR_variant | 7/7 | ENST00000634734.3 | ||
BAG1 | NM_001172415.2 | c.*1612G>C | 3_prime_UTR_variant | 7/7 | |||
BAG1 | NM_001349286.2 | c.*1612G>C | 3_prime_UTR_variant | 7/7 | |||
BAG1 | NM_001349299.2 | c.*1612G>C | 3_prime_UTR_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BAG1 | ENST00000634734.3 | c.*1612G>C | 3_prime_UTR_variant | 7/7 | 1 | NM_004323.6 | A2 | ||
BAG1 | ENST00000493917.5 | n.69+2258G>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.194 AC: 29372AN: 151754Hom.: 3088 Cov.: 30
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GnomAD4 exome AF: 0.250 AC: 1AN: 4Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 1AN XY: 4
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GnomAD4 genome ? AF: 0.194 AC: 29402AN: 151870Hom.: 3093 Cov.: 30 AF XY: 0.193 AC XY: 14357AN XY: 74258
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ClinVar
Not reported inComputational scores
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Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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