dbSNP rs12420140: BCO2:c.866-42G>A (chr11-112200571-G-A) – 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.866-42G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 1,560,866 control chromosomes in the GnomAD database, including 52,254 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 0.19 ( 3600 hom., cov: 32)

Exomes 𝑓: 0.25 ( 48654 hom. )

Consequence

BCO2
NM_031938.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.584

Publications

15 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=-0.72).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BCO2	NM_031938.7 link	c.866-42G>A		intron_variant	Intron 6 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.866-42G>A		intron_variant	Intron 6 of 11	1	NM_031938.7	ENSP00000350314.5		Q9BYV7-1

Frequencies

GnomAD3 genomes

AF:

0.189

AC:

28708

AN:

151996

Hom.:

3597

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0514

Gnomad AMI

AF:

0.347

Gnomad AMR

AF:

0.228

Gnomad ASJ

AF:

0.138

Gnomad EAS

AF:

0.00539

Gnomad SAS

AF:

0.0935

Gnomad FIN

AF:

0.267

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.274

Gnomad OTH

AF:

0.174

GnomAD2 exomes

AF:

0.206

AC:

46510

AN:

225996

AF XY:

0.204

show subpopulations

Gnomad AFR exome

AF:

0.0459

Gnomad AMR exome

AF:

0.264

Gnomad ASJ exome

AF:

0.142

Gnomad EAS exome

AF:

0.00221

Gnomad FIN exome

AF:

0.268

Gnomad NFE exome

AF:

0.267

Gnomad OTH exome

AF:

0.208

GnomAD4 exome

AF:

0.251

AC:

353865

AN:

1408752

Hom.:

48654

Cov.:

AF XY:

0.246

AC XY:

172599

AN XY:

700778

show subpopulations

African (AFR)

AF:

0.0376

AC:

1167

AN:

31012

American (AMR)

AF:

0.262

AC:

9393

AN:

35886

Ashkenazi Jewish (ASJ)

AF:

0.143

AC:

3518

AN:

24662

East Asian (EAS)

AF:

0.00507

AC:

198

AN:

39044

South Asian (SAS)

AF:

0.0982

AC:

7938

AN:

80794

European-Finnish (FIN)

AF:

0.274

AC:

14445

AN:

52758

Middle Eastern (MID)

AF:

0.121

AC:

675

AN:

5582

European-Non Finnish (NFE)

AF:

0.281

AC:

303778

AN:

1080618

Other (OTH)

AF:

0.218

AC:

12753

AN:

58396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

12476

24952

37428

49904

62380

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9806

19612

29418

39224

49030

<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:

0.189

AC:

28714

AN:

152114

Hom.:

3600

Cov.:

AF XY:

0.185

AC XY:

13778

AN XY:

74340

show subpopulations

African (AFR)

AF:

0.0513

AC:

2130

AN:

41528

American (AMR)

AF:

0.228

AC:

3491

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.138

AC:

479

AN:

3468

East Asian (EAS)

AF:

0.00521

AC:

AN:

5180

South Asian (SAS)

AF:

0.0940

AC:

454

AN:

4830

European-Finnish (FIN)

AF:

0.267

AC:

2810

AN:

10542

Middle Eastern (MID)

AF:

0.167

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.274

AC:

18595

AN:

67964

Other (OTH)

AF:

0.172

AC:

364

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1126

2252

3378

4504

5630

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

310

620

930

1240

1550

<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:

0.239

Hom.:

3655

Bravo

AF:

0.183

Asia WGS

AF:

0.0440

AC:

151

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

8.2

(source)

DANN

Benign

0.77

PhyloP100

-0.58

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