NM_031938.7:c.1333-169T>C

Variant names:

• chr11-112214593-T-C
• rs2250417
• NM_031938.7:c.1333-169T>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.1333-169T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.458 in 588,248 control chromosomes in the GnomAD database, including 66,540 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 0.43 (15505 hom., cov: 33)
  • Exomes 𝑓: 0.47 (51035 hom.)
• Consequence: BCO2 NM_031938.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 45 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]

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 = 0.528 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031938.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCO2	NM_031938.7	MANE Select	c.1333-169T>C		intron	N/A	NP_114144.5
	BCO2	NM_001037290.4		c.1231-169T>C		intron	N/A	NP_001032367.3
	BCO2	NM_001256397.3		c.1231-169T>C		intron	N/A	NP_001243326.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCO2	ENST00000357685.11	TSL:1 MANE Select	c.1333-169T>C		intron	N/A	ENSP00000350314.5
	BCO2	ENST00000438022.5	TSL:1	c.1231-169T>C		intron	N/A	ENSP00000414843.1
	BCO2	ENST00000531169.5	TSL:1	c.1231-169T>C		intron	N/A	ENSP00000437053.1

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65926 AN: 152036 Hom.: 15502 Cov.: 33

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.424

GnomAD4 exome AF: 0.467 AC: 203579 AN: 436094 Hom.: 51035 AF XY: 0.459 AC XY: 104874 AN XY: 228564

African (AFR) AF: 0.269 AC: 3301 AN: 12270

American (AMR) AF: 0.501 AC: 8509 AN: 16996

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 5142 AN: 13460

East Asian (EAS) AF: 0.137 AC: 4199 AN: 30722

South Asian (SAS) AF: 0.316 AC: 12802 AN: 40516

European-Finnish (FIN) AF: 0.559 AC: 16277 AN: 29132

Middle Eastern (MID) AF: 0.346 AC: 668 AN: 1930

European-Non Finnish (NFE) AF: 0.531 AC: 140981 AN: 265676

Other (OTH) AF: 0.461 AC: 11700 AN: 25392

GnomAD4 genome AF: 0.433 AC: 65923 AN: 152154 Hom.: 15505 Cov.: 33 AF XY: 0.430 AC XY: 31996 AN XY: 74374

African (AFR) AF: 0.276 AC: 11438 AN: 41500

American (AMR) AF: 0.476 AC: 7270 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1339 AN: 3470

East Asian (EAS) AF: 0.139 AC: 723 AN: 5188

South Asian (SAS) AF: 0.304 AC: 1464 AN: 4820

European-Finnish (FIN) AF: 0.562 AC: 5950 AN: 10582

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.532 AC: 36195 AN: 67990

Other (OTH) AF: 0.418 AC: 884 AN: 2114

Alfa AF: 0.491 Hom.: 87697

Bravo AF: 0.424

Asia WGS AF: 0.236 AC: 823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.0
DANN	Benign	0.52
PhyloP100		0.21
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: rs2250417; hg19: chr11-112085316;