rs7105056

Positions:

• chr11-112193708-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.517+11T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.978 in 1,608,290 control chromosomes in the GnomAD database, including 769,231 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 0.95 (68909 hom., cov: 33)
  • Exomes 𝑓: 0.98 (700322 hom.)
• Consequence: BCO2 NM_031938.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.150

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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.978 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BCO2	NM_031938.7	c.517+11T>C		intron_variant		ENST00000357685.11	NP_114144.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BCO2	ENST00000357685.11	c.517+11T>C		intron_variant		1	NM_031938.7	ENSP00000350314	P2

Frequencies

GnomAD3 genomes AF: 0.950 AC: 144563 AN: 152194 Hom.: 68868 Cov.: 33

Gnomad AFR AF: 0.871

Gnomad AMI AF: 0.992

Gnomad AMR AF: 0.970

Gnomad ASJ AF: 0.941

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.953

Gnomad FIN AF: 0.982

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.984

Gnomad OTH AF: 0.953

GnomAD3 exomes AF: 0.971 AC: 239216 AN: 246290 Hom.: 116330 AF XY: 0.972 AC XY: 129208 AN XY: 132956

Gnomad AFR exome AF: 0.865

Gnomad AMR exome AF: 0.986

Gnomad ASJ exome AF: 0.937

Gnomad EAS exome AF: 1.00

Gnomad SAS exome AF: 0.949

Gnomad FIN exome AF: 0.984

Gnomad NFE exome AF: 0.984

Gnomad OTH exome AF: 0.974

GnomAD4 exome AF: 0.981 AC: 1427642 AN: 1455978 Hom.: 700322 Cov.: 35 AF XY: 0.980 AC XY: 709561 AN XY: 724162

Gnomad4 AFR exome AF: 0.864

Gnomad4 AMR exome AF: 0.984

Gnomad4 ASJ exome AF: 0.937

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.950

Gnomad4 FIN exome AF: 0.983

Gnomad4 NFE exome AF: 0.987

Gnomad4 OTH exome AF: 0.972

GnomAD4 genome AF: 0.950 AC: 144661 AN: 152312 Hom.: 68909 Cov.: 33 AF XY: 0.951 AC XY: 70856 AN XY: 74478

Gnomad4 AFR AF: 0.871

Gnomad4 AMR AF: 0.970

Gnomad4 ASJ AF: 0.941

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.953

Gnomad4 FIN AF: 0.982

Gnomad4 NFE AF: 0.984

Gnomad4 OTH AF: 0.954

Alfa AF: 0.977 Hom.: 151768

Bravo AF: 0.947

Asia WGS AF: 0.969 AC: 3372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	10
DANN	Benign	0.48

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: rs7105056; hg19: chr11-112064431;