16-81239178-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_017429.3(BCO1):c.64+206G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0303 in 151,716 control chromosomes in the GnomAD database, including 83 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.030 (83 hom., cov: 31)
• Consequence: BCO1 NM_017429.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.365

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BP6: Variant 16-81239178-G-A is Benign according to our data. Variant chr16-81239178-G-A is described in ClinVar as [Benign]. Clinvar id is 1289541.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BCO1	NM_017429.3	c.64+206G>A		intron_variant		ENST00000258168.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCO1	ENST00000258168.7	c.64+206G>A		intron_variant		1	NM_017429.3	P1
BCO1	ENST00000564552.1	c.64+206G>A		intron_variant		2
BCO1	ENST00000563804.5	c.64+206G>A		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0302 AC: 4582 AN: 151600 Hom.: 83 Cov.: 31

Gnomad AFR AF: 0.0595

Gnomad AMI AF: 0.00549

Gnomad AMR AF: 0.0211

Gnomad ASJ AF: 0.0286

Gnomad EAS AF: 0.000774

Gnomad SAS AF: 0.0283

Gnomad FIN AF: 0.0110

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0204

Gnomad OTH AF: 0.0250

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0303 AC: 4592 AN: 151716 Hom.: 83 Cov.: 31 AF XY: 0.0282 AC XY: 2089 AN XY: 74096

Gnomad4 AFR AF: 0.0596

Gnomad4 AMR AF: 0.0210

Gnomad4 ASJ AF: 0.0286

Gnomad4 EAS AF: 0.000776

Gnomad4 SAS AF: 0.0281

Gnomad4 FIN AF: 0.0110

Gnomad4 NFE AF: 0.0204

Gnomad4 OTH AF: 0.0248

Alfa AF: 0.0265 Hom.: 10

Bravo AF: 0.0321

Asia WGS AF: 0.0160 AC: 55 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 18, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.8
Dann	Benign	0.53

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

Other links and lift over

dbSNP: rs116897482; hg19: chr16-81272783;