dbSNP rs11214139: BCO2:c.1515+210A>G (chr11-112215154-A-G) – 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.1515+210A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 558,744 control chromosomes in the GnomAD database, including 6,571 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 0.10 ( 1232 hom., cov: 32)

Exomes 𝑓: 0.13 ( 5339 hom. )

Consequence

BCO2
NM_031938.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.10

Publications

6 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:

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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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.375 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.1515+210A>G	intron	N/A	NP_114144.5
BCO2	NM_001037290.4		c.1413+210A>G	intron	N/A	NP_001032367.3
BCO2	NM_001256397.3		c.1395+228A>G	intron	N/A	NP_001243326.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
BCO2	ENST00000357685.11	TSL:1 MANE Select	c.1515+210A>G	intron	N/A	ENSP00000350314.5
BCO2	ENST00000438022.5	TSL:1	c.1413+210A>G	intron	N/A	ENSP00000414843.1
BCO2	ENST00000531169.5	TSL:1	c.1413+210A>G	intron	N/A	ENSP00000437053.1

Frequencies

GnomAD3 genomes

AF:

0.103

AC:

15702

AN:

152026

Hom.:

1235

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0244

Gnomad AMI

AF:

0.181

Gnomad AMR

AF:

0.109

Gnomad ASJ

AF:

0.162

Gnomad EAS

AF:

0.388

Gnomad SAS

AF:

0.0561

Gnomad FIN

AF:

0.163

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.118

Gnomad OTH

AF:

0.122

GnomAD4 exome

AF:

0.133

AC:

54130

AN:

406600

Hom.:

5339

Cov.:

AF XY:

0.129

AC XY:

27738

AN XY:

215040

show subpopulations

African (AFR)

AF:

0.0244

AC:

282

AN:

11558

American (AMR)

AF:

0.106

AC:

1645

AN:

15582

Ashkenazi Jewish (ASJ)

AF:

0.171

AC:

2118

AN:

12416

East Asian (EAS)

AF:

0.435

AC:

12041

AN:

27680

South Asian (SAS)

AF:

0.0498

AC:

2082

AN:

41778

European-Finnish (FIN)

AF:

0.164

AC:

3924

AN:

23946

Middle Eastern (MID)

AF:

0.131

AC:

231

AN:

1766

European-Non Finnish (NFE)

AF:

0.116

AC:

28864

AN:

248420

Other (OTH)

AF:

0.125

AC:

2943

AN:

23454

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

2022

4043

6065

8086

10108

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

248

496

744

992

1240

<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:

0.103

AC:

15696

AN:

152144

Hom.:

1232

Cov.:

AF XY:

0.107

AC XY:

7971

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.0244

AC:

1013

AN:

41534

American (AMR)

AF:

0.109

AC:

1659

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.162

AC:

561

AN:

3470

East Asian (EAS)

AF:

0.389

AC:

2008

AN:

5158

South Asian (SAS)

AF:

0.0561

AC:

271

AN:

4828

European-Finnish (FIN)

AF:

0.163

AC:

1721

AN:

10574

Middle Eastern (MID)

AF:

0.150

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.118

AC:

8001

AN:

67976

Other (OTH)

AF:

0.120

AC:

254

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

687

1374

2060

2747

3434

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

170

340

510

680

850

<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:

0.0968

Hom.:

576

Bravo

AF:

0.0994

Asia WGS

AF:

0.171

AC:

595

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.026

(source)

DANN

Benign

0.33

PhyloP100

-2.1

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over