rs11214139

chr11-112215154-A-G

Variant summary

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

The NM_031938.7(BCO2):c.1515+210A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 558,744 control chromosomes in the GnomAD database, including 6,571 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 0.10 (1232 hom., cov: 32)
  • Exomes 𝑓: 0.13 (5339 hom.)
• Consequence: BCO2 NM_031938.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.10

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 = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BCO2	NM_031938.7	c.1515+210A>G		intron_variant		ENST00000357685.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCO2	ENST00000357685.11	c.1515+210A>G		intron_variant		1	NM_031938.7	P2

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15702 AN: 152026 Hom.: 1235 Cov.: 32

Gnomad AFR AF: 0.0244

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.0561

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.122

GnomAD4 exome AF: 0.133 AC: 54130 AN: 406600 Hom.: 5339 Cov.: 4 AF XY: 0.129 AC XY: 27738 AN XY: 215040

Gnomad4 AFR exome AF: 0.0244

Gnomad4 AMR exome AF: 0.106

Gnomad4 ASJ exome AF: 0.171

Gnomad4 EAS exome AF: 0.435

Gnomad4 SAS exome AF: 0.0498

Gnomad4 FIN exome AF: 0.164

Gnomad4 NFE exome AF: 0.116

Gnomad4 OTH exome AF: 0.125

GnomAD4 genome AF: 0.103 AC: 15696 AN: 152144 Hom.: 1232 Cov.: 32 AF XY: 0.107 AC XY: 7971 AN XY: 74388

Gnomad4 AFR AF: 0.0244

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.0561

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.120

Alfa AF: 0.107 Hom.: 494

Bravo AF: 0.0994

Asia WGS AF: 0.171 AC: 595 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	0.026
Dann	Benign	0.33

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: rs11214139; hg19: chr11-112085877;