rs1367038

Variant names:

• chr11-112220576-G-T
• rs1367038
• ENST00000531169.5:c.*15+2687G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCO2	ENST00000531169.5	c.*15+2687G>T		intron_variant	Intron 12 of 12	1		ENSP00000437053.1

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

African (AFR) AF: 0.534 AC: 22136 AN: 41458

American (AMR) AF: 0.731 AC: 11170 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.746 AC: 2587 AN: 3470

East Asian (EAS) AF: 0.800 AC: 4147 AN: 5184

South Asian (SAS) AF: 0.768 AC: 3709 AN: 4828

European-Finnish (FIN) AF: 0.704 AC: 7434 AN: 10562

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.714 AC: 48543 AN: 67964

Other (OTH) AF: 0.678 AC: 1432 AN: 2112

Alfa AF: 0.701 Hom.: 57488

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
PhyloP100		0.53
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1367038; hg19: chr11-112091299;