rs2250417

chr11-112214593-T-C

Variant summary

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

The NM_031938.7(BCO2):c.1333-169T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.458 in 588,248 control chromosomes in the GnomAD database, including 66,540 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 0.43 (15505 hom., cov: 33)
  • Exomes 𝑓: 0.47 (51035 hom.)
• Consequence: BCO2 NM_031938.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

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 = 0.528 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BCO2	NM_031938.7	c.1333-169T>C		intron_variant		ENST00000357685.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCO2	ENST00000357685.11	c.1333-169T>C		intron_variant		1	NM_031938.7	P2

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65926 AN: 152036 Hom.: 15502 Cov.: 33

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.424

GnomAD4 exome AF: 0.467 AC: 203579 AN: 436094 Hom.: 51035 AF XY: 0.459 AC XY: 104874 AN XY: 228564

Gnomad4 AFR exome AF: 0.269

Gnomad4 AMR exome AF: 0.501

Gnomad4 ASJ exome AF: 0.382

Gnomad4 EAS exome AF: 0.137

Gnomad4 SAS exome AF: 0.316

Gnomad4 FIN exome AF: 0.559

Gnomad4 NFE exome AF: 0.531

Gnomad4 OTH exome AF: 0.461

GnomAD4 genome AF: 0.433 AC: 65923 AN: 152154 Hom.: 15505 Cov.: 33 AF XY: 0.430 AC XY: 31996 AN XY: 74374

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.476

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.562

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.418

Alfa AF: 0.498 Hom.: 44146

Bravo AF: 0.424

Asia WGS AF: 0.236 AC: 823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	5.0
Dann	Benign	0.52

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: rs2250417; hg19: chr11-112085316;