rs45474992
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBS1BS2
The NM_014417.5(BBC3):c.*495G>A variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.0238 in 173,826 control chromosomes in the GnomAD database, including 79 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 0.024 ( 67 hom., cov: 30)
Exomes 𝑓: 0.024 ( 12 hom. )
Consequence
BBC3
NM_014417.5 3_prime_UTR
NM_014417.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.84
Genes affected
BBC3 (HGNC:17868): (BCL2 binding component 3) This gene encodes a member of the BCL-2 family of proteins. This family member belongs to the BH3-only pro-apoptotic subclass. The protein cooperates with direct activator proteins to induce mitochondrial outer membrane permeabilization and apoptosis. It can bind to anti-apoptotic Bcl-2 family members to induce mitochondrial dysfunction and caspase activation. Because of its pro-apoptotic role, this gene is a potential drug target for cancer therapy and for tissue injury. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.35).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0238 (3612/152008) while in subpopulation NFE AF= 0.0343 (2327/67934). AF 95% confidence interval is 0.0331. There are 67 homozygotes in gnomad4. There are 1737 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 67 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BBC3 | NM_014417.5 | c.*495G>A | 3_prime_UTR_variant | 4/4 | ENST00000439096.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BBC3 | ENST00000439096.3 | c.*495G>A | 3_prime_UTR_variant | 4/4 | 1 | NM_014417.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0238 AC: 3614AN: 151892Hom.: 67 Cov.: 30
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GnomAD4 exome AF: 0.0244 AC: 532AN: 21818Hom.: 12 Cov.: 0 AF XY: 0.0251 AC XY: 286AN XY: 11412
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GnomAD4 genome ? AF: 0.0238 AC: 3612AN: 152008Hom.: 67 Cov.: 30 AF XY: 0.0234 AC XY: 1737AN XY: 74300
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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