rs10891337

Variant names:

• chr11-112192531-C-T
• rs10891337
• NM_031938.7:c.294-943C>T

Variant summary

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

The NM_031938.7(BCO2):​c.294-943C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 151,816 control chromosomes in the GnomAD database, including 4,089 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 0.23 (4089 hom., cov: 31)
• Consequence: BCO2 NM_031938.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229
• Publications: 13 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]

ENSG00000255292 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BCO2	NM_031938.7	c.294-943C>T		intron_variant	Intron 2 of 11	ENST00000357685.11	NP_114144.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCO2	ENST00000357685.11	c.294-943C>T		intron_variant	Intron 2 of 11	1	NM_031938.7	ENSP00000350314.5
ENSG00000255292	ENST00000532699.1	n.*56-943C>T		intron_variant	Intron 5 of 5	3		ENSP00000456434.1

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34773 AN: 151698 Hom.: 4091 Cov.: 31

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.229 AC: 34757 AN: 151816 Hom.: 4089 Cov.: 31 AF XY: 0.230 AC XY: 17052 AN XY: 74144

African (AFR) AF: 0.194 AC: 8015 AN: 41384

American (AMR) AF: 0.236 AC: 3604 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 828 AN: 3466

East Asian (EAS) AF: 0.134 AC: 695 AN: 5178

South Asian (SAS) AF: 0.201 AC: 966 AN: 4810

European-Finnish (FIN) AF: 0.283 AC: 2970 AN: 10510

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16904 AN: 67896

Other (OTH) AF: 0.230 AC: 484 AN: 2108

Alfa AF: 0.241 Hom.: 7815

Bravo AF: 0.225

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.6
DANN	Benign	0.59
PhyloP100		0.23
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10891337; hg19: chr11-112063254;