Variant 16-81245515-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_017429.3(BCO1):c.105T>C(p.Asn35Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 1,613,986 control chromosomes in the GnomAD database, including 92,120 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.39 ( 12062 hom., cov: 32)

Exomes 𝑓: 0.33 ( 80058 hom. )

Consequence

BCO1
NM_017429.3 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.69

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 16-81245515-T-C is Benign according to our data. Variant chr16-81245515-T-C is described in ClinVar as [Benign]. Clinvar id is 1250161.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-81245515-T-C is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-1.69 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.514 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.105T>C	p.Asn35Asn	synonymous_variant	2/11	ENST00000258168.7	NP_059125.2	Q9HAY6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
BCO1	ENST00000258168.7 linkuse as main transcript	c.105T>C	p.Asn35Asn	synonymous_variant	2/11	1	NM_017429.3	ENSP00000258168.2	Q9HAY6
BCO1	ENST00000564552.1 linkuse as main transcript	c.105T>C	p.Asn35Asn	synonymous_variant	2/4	2		ENSP00000455219.1	H3BPA2
BCO1	ENST00000563804.5 linkuse as main transcript	n.105T>C		non_coding_transcript_exon_variant	2/10	2		ENSP00000457910.1	H3BV18

Frequencies

GnomAD3 genomes

AF:

0.388

AC:

58960

AN:

152042

Hom.:

12036

Cov.:

show subpopulations

Gnomad AFR

AF:

0.519

Gnomad AMI

AF:

0.390

Gnomad AMR

AF:

0.350

Gnomad ASJ

AF:

0.366

Gnomad EAS

AF:

0.371

Gnomad SAS

AF:

0.273

Gnomad FIN

AF:

0.354

Gnomad MID

AF:

0.373

Gnomad NFE

AF:

0.334

Gnomad OTH

AF:

0.342

GnomAD3 exomes

AF:

0.336

AC:

84386

AN:

251440

Hom.:

14642

AF XY:

0.330

AC XY:

44846

AN XY:

135898

show subpopulations

Gnomad AFR exome

AF:

0.521

Gnomad AMR exome

AF:

0.302

Gnomad ASJ exome

AF:

0.351

Gnomad EAS exome

AF:

0.362

Gnomad SAS exome

AF:

0.272

Gnomad FIN exome

AF:

0.350

Gnomad NFE exome

AF:

0.328

Gnomad OTH exome

AF:

0.330

GnomAD4 exome

AF:

0.328

AC:

479487

AN:

1461826

Hom.:

80058

Cov.:

AF XY:

0.326

AC XY:

237159

AN XY:

727216

show subpopulations

Gnomad4 AFR exome

AF:

0.529

Gnomad4 AMR exome

AF:

0.309

Gnomad4 ASJ exome

AF:

0.344

Gnomad4 EAS exome

AF:

0.371

Gnomad4 SAS exome

AF:

0.273

Gnomad4 FIN exome

AF:

0.353

Gnomad4 NFE exome

AF:

0.323

Gnomad4 OTH exome

AF:

0.342

GnomAD4 genome

AF:

0.388

AC:

59024

AN:

152160

Hom.:

12062

Cov.:

AF XY:

0.386

AC XY:

28751

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.520

Gnomad4 AMR

AF:

0.349

Gnomad4 ASJ

AF:

0.366

Gnomad4 EAS

AF:

0.370

Gnomad4 SAS

AF:

0.272

Gnomad4 FIN

AF:

0.354

Gnomad4 NFE

AF:

0.334

Gnomad4 OTH

AF:

0.341

Alfa

AF:

0.355

Hom.:

5144

Bravo

AF:

0.391

Asia WGS

AF:

0.323

AC:

1124

AN:

3478

EpiCase

AF:

0.329

EpiControl

AF:

0.324

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_noAF

Benign

-0.83

CADD

Benign

0.013

DANN

Benign

0.39

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