rs12797880

chr11-112178468-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.89-810T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,224 control chromosomes in the GnomAD database, including 2,870 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 0.17 (2870 hom., cov: 32)
• Consequence: BCO2 NM_031938.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BCO2	NM_031938.7	c.89-810T>C		intron_variant		ENST00000357685.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCO2	ENST00000357685.11	c.89-810T>C		intron_variant		1	NM_031938.7	P2

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25428 AN: 152106 Hom.: 2869 Cov.: 32

Gnomad AFR AF: 0.0463

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.00538

Gnomad SAS AF: 0.0820

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.167 AC: 25426 AN: 152224 Hom.: 2870 Cov.: 32 AF XY: 0.163 AC XY: 12123 AN XY: 74408

Gnomad4 AFR AF: 0.0462

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.00520

Gnomad4 SAS AF: 0.0825

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.160

Alfa AF: 0.207 Hom.: 540

Bravo AF: 0.157

Asia WGS AF: 0.0400 AC: 138 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	7.2
Dann	Benign	0.82

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: rs12797880; hg19: chr11-112049191;