rs10891337

chr11-112192531-C-T

Variant summary

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

The NM_031938.7(BCO2):c.294-943C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 151,816 control chromosomes in the GnomAD database, including 4,089 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 0.23 (4089 hom., cov: 31)
• Consequence: BCO2 NM_031938.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BCO2	NM_031938.7	c.294-943C>T		intron_variant		ENST00000357685.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCO2	ENST00000357685.11	c.294-943C>T		intron_variant		1	NM_031938.7	P2

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34773 AN: 151698 Hom.: 4091 Cov.: 31

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.229 AC: 34757 AN: 151816 Hom.: 4089 Cov.: 31 AF XY: 0.230 AC XY: 17052 AN XY: 74144

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.230

Alfa AF: 0.241 Hom.: 2148

Bravo AF: 0.225

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.6
Dann	Benign	0.59

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10891337; hg19: chr11-112063254;