rs12420140
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_031938.7(BCO2):c.866-42G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 1,560,866 control chromosomes in the GnomAD database, including 52,254 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 ( 3600 hom., cov: 32)
Exomes 𝑓: 0.25 ( 48654 hom. )
Consequence
BCO2
NM_031938.7 intron
NM_031938.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.584
Genes affected
BCO2 (HGNC:18503): (beta-carotene oxygenase 2) This gene encodes an enzyme which oxidizes carotenoids such as beta-carotene during the biosynthesis of vitamin A. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]
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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=-0.72).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.189 AC: 28708AN: 151996Hom.: 3597 Cov.: 32
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GnomAD3 exomes AF: 0.206 AC: 46510AN: 225996Hom.: 6009 AF XY: 0.204 AC XY: 25182AN XY: 123226
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GnomAD4 exome AF: 0.251 AC: 353865AN: 1408752Hom.: 48654 Cov.: 26 AF XY: 0.246 AC XY: 172599AN XY: 700778
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GnomAD4 genome AF: 0.189 AC: 28714AN: 152114Hom.: 3600 Cov.: 32 AF XY: 0.185 AC XY: 13778AN XY: 74340
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at