rs3784296
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_016654.5(GABPB1):c.*1480A>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 0.518 in 151,938 control chromosomes in the GnomAD database, including 22,052 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 0.52 ( 22051 hom., cov: 32)
Exomes 𝑓: 1.0 ( 1 hom. )
Consequence
GABPB1
NM_016654.5 3_prime_UTR
NM_016654.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0360
Genes affected
GABPB1 (HGNC:4074): (GA binding protein transcription factor subunit beta 1) This gene encodes the GA-binding protein transcription factor, beta subunit. This protein forms a tetrameric complex with the alpha subunit, and stimulates transcription of target genes. The encoded protein may be involved in activation of cytochrome oxidase expression and nuclear control of mitochondrial function. The crystal structure of a similar protein in mouse has been resolved as a ternary protein complex. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
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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=-0.87).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GABPB1 | NM_016654.5 | c.*1480A>C | 3_prime_UTR_variant | 9/9 | ENST00000380877.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABPB1 | ENST00000380877.8 | c.*1480A>C | 3_prime_UTR_variant | 9/9 | 1 | NM_016654.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.518 AC: 78636AN: 151818Hom.: 22037 Cov.: 32
GnomAD3 genomes
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GnomAD4 exome AF: 1.00 AC: 2AN: 2Hom.: 1 Cov.: 0 AF XY: 1.00 AC XY: 2AN XY: 2
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GnomAD4 genome ? AF: 0.518 AC: 78686AN: 151936Hom.: 22051 Cov.: 32 AF XY: 0.510 AC XY: 37869AN XY: 74210
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ClinVar
Not reported inComputational scores
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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