rs12420140

Variant summary

Our verdict is Benign. Variant got -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

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.584
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons MANE Protein UniProt
BCO2NM_031938.7 linkc.866-42G>A intron_variant ENST00000357685.11 NP_114144.5 Q9BYV7-1B2RCV8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
BCO2ENST00000357685.11 linkc.866-42G>A intron_variant 1 NM_031938.7 ENSP00000350314.5 Q9BYV7-1

Frequencies

GnomAD3 genomes
AF:
0.189
AC:
28708
AN:
151996
Hom.:
3597
Cov.:
32
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
GnomAD3 exomes
AF:
0.206
AC:
46510
AN:
225996
Hom.:
6009
AF XY:
0.204
AC XY:
25182
AN XY:
123226
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 SAS exome
AF:
0.0941
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.:
26
AF XY:
0.246
AC XY:
172599
AN XY:
700778
show subpopulations
Gnomad4 AFR exome
AF:
0.0376
Gnomad4 AMR exome
AF:
0.262
Gnomad4 ASJ exome
AF:
0.143
Gnomad4 EAS exome
AF:
0.00507
Gnomad4 SAS exome
AF:
0.0982
Gnomad4 FIN exome
AF:
0.274
Gnomad4 NFE exome
AF:
0.281
Gnomad4 OTH exome
AF:
0.218
GnomAD4 genome
AF:
0.189
AC:
28714
AN:
152114
Hom.:
3600
Cov.:
32
AF XY:
0.185
AC XY:
13778
AN XY:
74340
show subpopulations
Gnomad4 AFR
AF:
0.0513
Gnomad4 AMR
AF:
0.228
Gnomad4 ASJ
AF:
0.138
Gnomad4 EAS
AF:
0.00521
Gnomad4 SAS
AF:
0.0940
Gnomad4 FIN
AF:
0.267
Gnomad4 NFE
AF:
0.274
Gnomad4 OTH
AF:
0.172
Alfa
AF:
0.237
Hom.:
2701
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
DANN
Benign
0.77

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs12420140; hg19: chr11-112071294; COSMIC: COSV63063187; API