rs12797880

Variant names:

• chr11-112178468-T-C
• rs12797880
• NM_031938.7:c.89-810T>C

Variant summary

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

The NM_031938.7(BCO2):​c.89-810T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,224 control chromosomes in the GnomAD database, including 2,870 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 0.17 (2870 hom., cov: 32)
• Consequence: BCO2 NM_031938.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19
• Publications: 6 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BCO2	NM_031938.7	c.89-810T>C		intron_variant	Intron 1 of 11	ENST00000357685.11	NP_114144.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCO2	ENST00000357685.11	c.89-810T>C		intron_variant	Intron 1 of 11	1	NM_031938.7	ENSP00000350314.5
ENSG00000255292	ENST00000532699.1	n.*55+7794T>C		intron_variant	Intron 5 of 5	3		ENSP00000456434.1

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25428 AN: 152106 Hom.: 2869 Cov.: 32

Gnomad AFR AF: 0.0463

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.00538

Gnomad SAS AF: 0.0820

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.167 AC: 25426 AN: 152224 Hom.: 2870 Cov.: 32 AF XY: 0.163 AC XY: 12123 AN XY: 74408

African (AFR) AF: 0.0462 AC: 1918 AN: 41552

American (AMR) AF: 0.142 AC: 2178 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 450 AN: 3472

East Asian (EAS) AF: 0.00520 AC: 27 AN: 5194

South Asian (SAS) AF: 0.0825 AC: 398 AN: 4826

European-Finnish (FIN) AF: 0.248 AC: 2627 AN: 10586

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.252 AC: 17138 AN: 67984

Other (OTH) AF: 0.160 AC: 339 AN: 2116

Alfa AF: 0.202 Hom.: 540

Bravo AF: 0.157

Asia WGS AF: 0.0400 AC: 138 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.2
DANN	Benign	0.82
PhyloP100		1.2
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: rs12797880; hg19: chr11-112049191;