rs2518356

Positions:

• chr11-112211770-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.1195-1954A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 152,088 control chromosomes in the GnomAD database, including 11,257 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 0.38 (11257 hom., cov: 33)
• Consequence: BCO2 NM_031938.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.423

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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BCO2	NM_031938.7	c.1195-1954A>G		intron_variant		ENST00000357685.11	NP_114144.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BCO2	ENST00000357685.11	c.1195-1954A>G		intron_variant		1	NM_031938.7	ENSP00000350314	P2

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57504 AN: 151970 Hom.: 11230 Cov.: 33

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.379 AC: 57569 AN: 152088 Hom.: 11257 Cov.: 33 AF XY: 0.380 AC XY: 28253 AN XY: 74344

Gnomad4 AFR AF: 0.456

Gnomad4 AMR AF: 0.369

Gnomad4 ASJ AF: 0.367

Gnomad4 EAS AF: 0.474

Gnomad4 SAS AF: 0.595

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.387

Alfa AF: 0.352 Hom.: 1190

Bravo AF: 0.385

Asia WGS AF: 0.553 AC: 1922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
DANN	Benign	0.45

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: rs2518356; hg19: chr11-112082493;