dbSNP rs2250417: BCO2:c.1333-169T>C (chr11-112214593-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.212

Publications

45 publications found

Variant links:

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]

BCO2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BCO2	NM_031938.7 link	c.1333-169T>C		intron_variant	Intron 9 of 11	ENST00000357685.11	NP_114144.5	Q9BYV7-1B2RCV8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCO2	ENST00000357685.11 link	c.1333-169T>C		intron_variant	Intron 9 of 11	1	NM_031938.7	ENSP00000350314.5		Q9BYV7-1

Frequencies

GnomAD3 genomes

AF:

0.434

AC:

65926

AN:

152036

Hom.:

15502

Cov.:

show subpopulations

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

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

4815

9630

14445

19260

24075

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

650

1300

1950

2600

3250

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.433

AC:

65923

AN:

152154

Hom.:

15505

Cov.:

AF XY:

0.430

AC XY:

31996

AN XY:

74374

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1849

3698

5546

7395

9244

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

612

1224

1836

2448

3060

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

5.0

(source)

DANN

Benign

0.52

PhyloP100

0.21

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over