rs4935984

chr11-112202207-G-A

Variant summary

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

The NM_031938.7(BCO2):c.1194+17G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 1,585,034 control chromosomes in the GnomAD database, including 104,713 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 (11255 hom., cov: 31)
  • Exomes 𝑓: 0.35 (93458 hom.)
• Consequence: BCO2 NM_031938.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.503

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=-0.73).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BCO2	NM_031938.7	c.1194+17G>A		intron_variant		ENST00000357685.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCO2	ENST00000357685.11	c.1194+17G>A		intron_variant		1	NM_031938.7	P2

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57488 AN: 151830 Hom.: 11228 Cov.: 31

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.379

GnomAD3 exomes AF: 0.381 AC: 86236 AN: 226574 Hom.: 17469 AF XY: 0.387 AC XY: 47540 AN XY: 122880

Gnomad AFR exome AF: 0.454

Gnomad AMR exome AF: 0.366

Gnomad ASJ exome AF: 0.365

Gnomad EAS exome AF: 0.478

Gnomad SAS exome AF: 0.583

Gnomad FIN exome AF: 0.259

Gnomad NFE exome AF: 0.335

Gnomad OTH exome AF: 0.370

GnomAD4 exome AF: 0.354 AC: 507312 AN: 1433086 Hom.: 93458 Cov.: 30 AF XY: 0.360 AC XY: 256841 AN XY: 712804

Gnomad4 AFR exome AF: 0.470

Gnomad4 AMR exome AF: 0.365

Gnomad4 ASJ exome AF: 0.360

Gnomad4 EAS exome AF: 0.437

Gnomad4 SAS exome AF: 0.578

Gnomad4 FIN exome AF: 0.263

Gnomad4 NFE exome AF: 0.334

Gnomad4 OTH exome AF: 0.373

GnomAD4 genome AF: 0.379 AC: 57554 AN: 151948 Hom.: 11255 Cov.: 31 AF XY: 0.380 AC XY: 28254 AN XY: 74282

Gnomad4 AFR AF: 0.456

Gnomad4 AMR AF: 0.369

Gnomad4 ASJ AF: 0.367

Gnomad4 EAS AF: 0.473

Gnomad4 SAS AF: 0.596

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.387

Alfa AF: 0.350 Hom.: 3308

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	-0.73
Cadd	Benign	13
Dann	Benign	0.70

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: rs4935984; hg19: chr11-112072930; COSMIC: COSV63064517; COSMIC: COSV63064517;