11-112220671-T-C

Variant names:

• chr11-112220671-T-C
• rs2518345
• ENST00000531169.5:c.*15+2782T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000531169.5(BCO2):​c.*15+2782T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 152,158 control chromosomes in the GnomAD database, including 39,400 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 0.72 (39400 hom., cov: 33)
• Consequence: BCO2 ENST00000531169.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.302
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.777 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000531169.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCO2	ENST00000531169.5	TSL:1	c.*15+2782T>C		intron	N/A	ENSP00000437053.1
	BCO2	ENST00000958916.1		c.*1055T>C		3_prime_UTR	Exon 13 of 13	ENSP00000628975.1
	BCO2	ENST00000856015.1		c.*15+2782T>C		intron	N/A	ENSP00000526074.1

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109257 AN: 152040 Hom.: 39353 Cov.: 33

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.752

Gnomad AMR AF: 0.756

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.723

Gnomad OTH AF: 0.720

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

GnomAD4 genome AF: 0.719 AC: 109367 AN: 152158 Hom.: 39400 Cov.: 33 AF XY: 0.719 AC XY: 53474 AN XY: 74384

African (AFR) AF: 0.682 AC: 28299 AN: 41506

American (AMR) AF: 0.757 AC: 11576 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.763 AC: 2645 AN: 3468

East Asian (EAS) AF: 0.797 AC: 4138 AN: 5192

South Asian (SAS) AF: 0.770 AC: 3710 AN: 4818

European-Finnish (FIN) AF: 0.705 AC: 7460 AN: 10576

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.723 AC: 49129 AN: 67982

Other (OTH) AF: 0.719 AC: 1522 AN: 2116

Alfa AF: 0.717 Hom.: 6957

Bravo AF: 0.720

Asia WGS AF: 0.754 AC: 2622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.0
DANN	Benign	0.63
PhyloP100		0.30
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2518345; hg19: chr11-112091394;