11-112216401-C-T

Variant names:

• chr11-112216401-C-T
• rs7938116
• NM_031938.7:c.1626+71C>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.1626+71C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0169 in 1,091,838 control chromosomes in the GnomAD database, including 766 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 0.048 (434 hom., cov: 33)
  • Exomes 𝑓: 0.012 (332 hom.)
• Consequence: BCO2 NM_031938.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.606
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BCO2	NM_031938.7	c.1626+71C>T		intron_variant	Intron 11 of 11	ENST00000357685.11	NP_114144.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCO2	ENST00000357685.11	c.1626+71C>T		intron_variant	Intron 11 of 11	1	NM_031938.7	ENSP00000350314.5

Frequencies

GnomAD3 genomes AF: 0.0475 AC: 7220 AN: 152130 Hom.: 433 Cov.: 33

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0249

Gnomad ASJ AF: 0.0167

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00186

Gnomad FIN AF: 0.00170

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00808

Gnomad OTH AF: 0.0445

GnomAD4 exome AF: 0.0119 AC: 11221 AN: 939590 Hom.: 332 AF XY: 0.0110 AC XY: 5342 AN XY: 486842

African (AFR) AF: 0.150 AC: 3517 AN: 23378

American (AMR) AF: 0.0171 AC: 695 AN: 40632

Ashkenazi Jewish (ASJ) AF: 0.0147 AC: 325 AN: 22036

East Asian (EAS) AF: 0.0000807 AC: 3 AN: 37180

South Asian (SAS) AF: 0.00203 AC: 150 AN: 73850

European-Finnish (FIN) AF: 0.00175 AC: 88 AN: 50334

Middle Eastern (MID) AF: 0.0295 AC: 139 AN: 4712

European-Non Finnish (NFE) AF: 0.00849 AC: 5475 AN: 644586

Other (OTH) AF: 0.0193 AC: 829 AN: 42882

GnomAD4 genome AF: 0.0476 AC: 7249 AN: 152248 Hom.: 434 Cov.: 33 AF XY: 0.0451 AC XY: 3359 AN XY: 74438

African (AFR) AF: 0.148 AC: 6132 AN: 41530

American (AMR) AF: 0.0249 AC: 380 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0167 AC: 58 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.00166 AC: 8 AN: 4822

European-Finnish (FIN) AF: 0.00170 AC: 18 AN: 10614

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00810 AC: 551 AN: 68026

Other (OTH) AF: 0.0440 AC: 93 AN: 2114

Alfa AF: 0.0482 Hom.: 73

Bravo AF: 0.0527

Asia WGS AF: 0.0140 AC: 48 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.27
DANN	Benign	0.61
PhyloP100		-0.61
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: rs7938116; hg19: chr11-112087124;