Genetic Variant 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.

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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
BCO2	NM_031938.7	MANE Select	c.866-42G>A	intron	N/A	NP_114144.5
BCO2	NM_001037290.4		c.764-42G>A	intron	N/A	NP_001032367.3
BCO2	NM_001256397.3		c.764-42G>A	intron	N/A	NP_001243326.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
BCO2	ENST00000357685.11	TSL:1 MANE Select	c.866-42G>A	intron	N/A	ENSP00000350314.5
BCO2	ENST00000438022.5	TSL:1	c.764-42G>A	intron	N/A	ENSP00000414843.1
BCO2	ENST00000531169.5	TSL:1	c.764-42G>A	intron	N/A	ENSP00000437053.1

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 v4.9

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over