dbSNP rs4935984: BCO2:c.1194+17G>A (chr11-112202207-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.1194+17G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 1,585,034 control chromosomes in the GnomAD database, including 104,713 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 0.38 ( 11255 hom., cov: 31)

Exomes 𝑓: 0.35 ( 93458 hom. )

Consequence

BCO2
NM_031938.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.503

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=-0.73).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.578 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.1194+17G>A	intron	N/A	NP_114144.5
BCO2	NM_001037290.4		c.1092+17G>A	intron	N/A	NP_001032367.3
BCO2	NM_001256397.3		c.1092+17G>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.1194+17G>A	intron	N/A	ENSP00000350314.5
BCO2	ENST00000438022.5	TSL:1	c.1092+17G>A	intron	N/A	ENSP00000414843.1
BCO2	ENST00000531169.5	TSL:1	c.1092+17G>A	intron	N/A	ENSP00000437053.1

Frequencies

GnomAD3 genomes

AF:

0.379

AC:

57488

AN:

151830

Hom.:

11228

Cov.:

show subpopulations

Gnomad AFR

AF:

0.456

Gnomad AMI

AF:

0.251

Gnomad AMR

AF:

0.369

Gnomad ASJ

AF:

0.367

Gnomad EAS

AF:

0.473

Gnomad SAS

AF:

0.595

Gnomad FIN

AF:

0.259

Gnomad MID

AF:

0.402

Gnomad NFE

AF:

0.332

Gnomad OTH

AF:

0.379

GnomAD2 exomes

AF:

0.381

AC:

86236

AN:

226574

AF XY:

0.387

show subpopulations

Gnomad AFR exome

AF:

0.454

Gnomad AMR exome

AF:

0.366

Gnomad ASJ exome

AF:

0.365

Gnomad EAS exome

AF:

0.478

Gnomad FIN exome

AF:

0.259

Gnomad NFE exome

AF:

0.335

Gnomad OTH exome

AF:

0.370

GnomAD4 exome

AF:

0.354

AC:

507312

AN:

1433086

Hom.:

93458

Cov.:

AF XY:

0.360

AC XY:

256841

AN XY:

712804

show subpopulations

African (AFR)

AF:

0.470

AC:

14858

AN:

31584

American (AMR)

AF:

0.365

AC:

13505

AN:

37024

Ashkenazi Jewish (ASJ)

AF:

0.360

AC:

8885

AN:

24656

East Asian (EAS)

AF:

0.437

AC:

17150

AN:

39230

South Asian (SAS)

AF:

0.578

AC:

47141

AN:

81562

European-Finnish (FIN)

AF:

0.263

AC:

13909

AN:

52968

Middle Eastern (MID)

AF:

0.426

AC:

2390

AN:

5610

European-Non Finnish (NFE)

AF:

0.334

AC:

367398

AN:

1101328

Other (OTH)

AF:

0.373

AC:

22076

AN:

59124

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.470

Heterozygous variant carriers

13626

27251

40877

54502

68128

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

12150

24300

36450

48600

60750

<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:

0.379

AC:

57554

AN:

151948

Hom.:

11255

Cov.:

AF XY:

0.380

AC XY:

28254

AN XY:

74282

show subpopulations

African (AFR)

AF:

0.456

AC:

18904

AN:

41444

American (AMR)

AF:

0.369

AC:

5644

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.367

AC:

1273

AN:

3468

East Asian (EAS)

AF:

0.473

AC:

2441

AN:

5164

South Asian (SAS)

AF:

0.596

AC:

2871

AN:

4816

European-Finnish (FIN)

AF:

0.259

AC:

2728

AN:

10538

Middle Eastern (MID)

AF:

0.388

AC:

114

AN:

294

European-Non Finnish (NFE)

AF:

0.332

AC:

22536

AN:

67930

Other (OTH)

AF:

0.387

AC:

815

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1806

3612

5419

7225

9031

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

560

1120

1680

2240

2800

<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:

0.350

Hom.:

3308

Bravo

AF:

0.385

Asia WGS

AF:

0.553

AC:

1922

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

(source)

DANN

Benign

0.70

PhyloP100

0.50

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