rs2115763

Positions:

• chr11-112180446-A-T

Variant summary

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

The NM_031938.7(BCO2):​c.293+964A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 152,116 control chromosomes in the GnomAD database, including 6,429 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 0.27 (6429 hom., cov: 32)
• Consequence: BCO2 NM_031938.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.38

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]

ENSG00000255292 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BCO2	NM_031938.7	c.293+964A>T		intron_variant		ENST00000357685.11	NP_114144.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BCO2	ENST00000357685.11	c.293+964A>T		intron_variant		1	NM_031938.7	ENSP00000350314.5
ENSG00000255292	ENST00000532699.1	n.*55+9772A>T		intron_variant		3		ENSP00000456434.1

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40630 AN: 152000 Hom.: 6423 Cov.: 32

Gnomad AFR AF: 0.0961

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.267 AC: 40637 AN: 152116 Hom.: 6429 Cov.: 32 AF XY: 0.272 AC XY: 20209 AN XY: 74356

Gnomad4 AFR AF: 0.0958

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.414

Gnomad4 SAS AF: 0.542

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.334

Gnomad4 OTH AF: 0.286

Alfa AF: 0.322 Hom.: 4507

Bravo AF: 0.251

Asia WGS AF: 0.451 AC: 1568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.5
DANN	Benign	0.81

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: rs2115763; hg19: chr11-112051169;