Variant chr16-81239023-T-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_017429.3(BCO1):c.64+51T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0251 in 1,415,534 control chromosomes in the GnomAD database, including 287 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.036 ( 103 hom., cov: 30)

Exomes 𝑓: 0.024 ( 184 hom. )

Consequence

BCO1
NM_017429.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.214

Variant links:

Genes affected

BCO1 (HGNC:13815): (beta-carotene oxygenase 1) Vitamin A metabolism is important for vital processes such as vision, embryonic development, cell differentiation, and membrane and skin protection. The protein encoded by this gene is a key enzyme in beta-carotene metabolism to vitamin A. It catalyzes the oxidative cleavage of beta,beta-carotene into two retinal molecules. [provided by RefSeq, Jul 2008]

BCO1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 16-81239023-T-A is Benign according to our data. Variant chr16-81239023-T-A is described in ClinVar as [Benign]. Clinvar id is 1267670.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BCO1	NM_017429.3 linkuse as main transcript	c.64+51T>A		intron_variant		ENST00000258168.7	NP_059125.2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
BCO1	ENST00000258168.7 linkuse as main transcript	c.64+51T>A	intron_variant	1	NM_017429.3	ENSP00000258168	P1
BCO1	ENST00000564552.1 linkuse as main transcript	c.64+51T>A	intron_variant	2		ENSP00000455219
BCO1	ENST00000563804.5 linkuse as main transcript	c.64+51T>A	intron_variant, NMD_transcript_variant	2		ENSP00000457910

Frequencies

GnomAD3 genomes

AF:

0.0363

AC:

5068

AN:

139450

Hom.:

103

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0780

Gnomad AMI

AF:

0.00552

Gnomad AMR

AF:

0.0230

Gnomad ASJ

AF:

0.0375

Gnomad EAS

AF:

0.00193

Gnomad SAS

AF:

0.0287

Gnomad FIN

AF:

0.0402

Gnomad MID

AF:

0.0397

Gnomad NFE

AF:

0.0230

Gnomad OTH

AF:

0.0300

GnomAD3 exomes

AF:

0.0326

AC:

4826

AN:

147846

Hom.:

AF XY:

0.0327

AC XY:

2713

AN XY:

82856

show subpopulations

Gnomad AFR exome

AF:

0.0991

Gnomad AMR exome

AF:

0.0171

Gnomad ASJ exome

AF:

0.0374

Gnomad EAS exome

AF:

0.000470

Gnomad SAS exome

AF:

0.0367

Gnomad FIN exome

AF:

0.0481

Gnomad NFE exome

AF:

0.0289

Gnomad OTH exome

AF:

0.0376

GnomAD4 exome

AF:

0.0239

AC:

30501

AN:

1276042

Hom.:

184

Cov.:

AF XY:

0.0244

AC XY:

15527

AN XY:

635868

show subpopulations

Gnomad4 AFR exome

AF:

0.0682

Gnomad4 AMR exome

AF:

0.0138

Gnomad4 ASJ exome

AF:

0.0331

Gnomad4 EAS exome

AF:

0.000360

Gnomad4 SAS exome

AF:

0.0306

Gnomad4 FIN exome

AF:

0.0395

Gnomad4 NFE exome

AF:

0.0223

Gnomad4 OTH exome

AF:

0.0268

GnomAD4 genome

AF:

0.0364

AC:

5078

AN:

139492

Hom.:

103

Cov.:

AF XY:

0.0353

AC XY:

2409

AN XY:

68278

show subpopulations

Gnomad4 AFR

AF:

0.0782

Gnomad4 AMR

AF:

0.0229

Gnomad4 ASJ

AF:

0.0375

Gnomad4 EAS

AF:

0.00194

Gnomad4 SAS

AF:

0.0285

Gnomad4 FIN

AF:

0.0402

Gnomad4 NFE

AF:

0.0230

Gnomad4 OTH

AF:

0.0297

Alfa

AF:

0.00975

Hom.:

Bravo

AF:

0.0341

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 18, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.88

DANN

Benign

0.17

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over