Variant chr16-81262297-T-C 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.471+14T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 1,608,542 control chromosomes in the GnomAD database, including 33,692 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.23 ( 4242 hom., cov: 30)

Exomes 𝑓: 0.20 ( 29450 hom. )

Consequence

BCO1
NM_017429.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.0120

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:

(HGNC:):

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 (MetaRNN=0.0042527616).

BP6

Variant 16-81262297-T-C is Benign according to our data. Variant chr16-81262297-T-C is described in ClinVar as [Benign]. Clinvar id is 1265199.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.285 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.471+14T>C		intron_variant		ENST00000258168.7	NP_059125.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
BCO1	ENST00000258168.7 linkuse as main transcript	c.471+14T>C		intron_variant		1	NM_017429.3	ENSP00000258168	P1
	ENST00000625028.1 linkuse as main transcript	n.1795A>G		non_coding_transcript_exon_variant	1/1
BCO1	ENST00000564552.1 linkuse as main transcript	c.485T>C	p.Met162Thr	missense_variant	4/4	2		ENSP00000455219
BCO1	ENST00000563804.5 linkuse as main transcript	c.*95+14T>C		intron_variant, NMD_transcript_variant		2		ENSP00000457910

Frequencies

GnomAD3 genomes

AF:

0.229

AC:

34749

AN:

151572

Hom.:

4242

Cov.:

show subpopulations

Gnomad AFR

AF:

0.289

Gnomad AMI

AF:

0.144

Gnomad AMR

AF:

0.273

Gnomad ASJ

AF:

0.246

Gnomad EAS

AF:

0.240

Gnomad SAS

AF:

0.189

Gnomad FIN

AF:

0.120

Gnomad MID

AF:

0.318

Gnomad NFE

AF:

0.202

Gnomad OTH

AF:

0.234

GnomAD3 exomes

AF:

0.211

AC:

53129

AN:

251368

Hom.:

5975

AF XY:

0.208

AC XY:

28239

AN XY:

135878

show subpopulations

Gnomad AFR exome

AF:

0.289

Gnomad AMR exome

AF:

0.259

Gnomad ASJ exome

AF:

0.238

Gnomad EAS exome

AF:

0.241

Gnomad SAS exome

AF:

0.171

Gnomad FIN exome

AF:

0.125

Gnomad NFE exome

AF:

0.206

Gnomad OTH exome

AF:

0.217

GnomAD4 exome

AF:

0.196

AC:

285880

AN:

1456852

Hom.:

29450

Cov.:

AF XY:

0.196

AC XY:

142152

AN XY:

725096

show subpopulations

Gnomad4 AFR exome

AF:

0.294

Gnomad4 AMR exome

AF:

0.260

Gnomad4 ASJ exome

AF:

0.235

Gnomad4 EAS exome

AF:

0.214

Gnomad4 SAS exome

AF:

0.171

Gnomad4 FIN exome

AF:

0.131

Gnomad4 NFE exome

AF:

0.193

Gnomad4 OTH exome

AF:

0.209

GnomAD4 genome

AF:

0.229

AC:

34768

AN:

151690

Hom.:

4242

Cov.:

AF XY:

0.226

AC XY:

16765

AN XY:

74108

show subpopulations

Gnomad4 AFR

AF:

0.289

Gnomad4 AMR

AF:

0.273

Gnomad4 ASJ

AF:

0.246

Gnomad4 EAS

AF:

0.240

Gnomad4 SAS

AF:

0.187

Gnomad4 FIN

AF:

0.120

Gnomad4 NFE

AF:

0.202

Gnomad4 OTH

AF:

0.232

Alfa

AF:

0.177

Hom.:

738

Bravo

AF:

0.242

TwinsUK

AF:

0.203

AC:

751

ALSPAC

AF:

0.198

AC:

763

ESP6500AA

AF:

0.291

AC:

1281

ESP6500EA

AF:

0.210

AC:

1805

ExAC

AF:

0.212

AC:

25735

Asia WGS

AF:

0.208

AC:

721

AN:

3478

EpiCase

AF:

0.216

EpiControl

AF:

0.225

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	Nov 10, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.47

BayesDel_noAF

Benign

-0.31

CADD

Benign

0.93

DANN

Benign

0.20

FATHMM_MKL

Benign

0.044

LIST_S2

Benign

0.20

MetaRNN

Benign

0.0043

MutationTaster

Benign

1.0

P;P;P

PROVEAN

Benign

0.52

Sift

Pathogenic

0.0

Vest4

0.056

GERP RS

-3.8

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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