rs1367038

Positions:

• chr11-112220576-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000531169.5(BCO2):​c.*15+2687G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.671 in 152,068 control chromosomes in the GnomAD database, including 34,827 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 0.67 (34827 hom., cov: 32)
• Consequence: BCO2 ENST00000531169.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.527

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCO2	ENST00000531169.5	c.*15+2687G>T		intron_variant		1		A2

Frequencies

GnomAD3 genomes AF: 0.671 AC: 101948 AN: 151950 Hom.: 34798 Cov.: 32

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.799

Gnomad SAS AF: 0.767

Gnomad FIN AF: 0.704

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.678

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.671 AC: 102036 AN: 152068 Hom.: 34827 Cov.: 32 AF XY: 0.674 AC XY: 50090 AN XY: 74344

Gnomad4 AFR AF: 0.534

Gnomad4 AMR AF: 0.731

Gnomad4 ASJ AF: 0.746

Gnomad4 EAS AF: 0.800

Gnomad4 SAS AF: 0.768

Gnomad4 FIN AF: 0.704

Gnomad4 NFE AF: 0.714

Gnomad4 OTH AF: 0.678

Alfa AF: 0.707 Hom.: 40563

Bravo AF: 0.667

Asia WGS AF: 0.742 AC: 2582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.55
DANN	Benign	0.74

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1367038; hg19: chr11-112091299;