16-81245849-C-CT

Position:

• chr16-81245849-C-CT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_017429.3(BCO1):​c.193+272dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.32 (8564 hom., cov: 0)
• Consequence: BCO1 NM_017429.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.889

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 -10 ACMG points.

• BP6: Variant 16-81245849-C-CT is Benign according to our data. Variant chr16-81245849-C-CT is described in ClinVar as [Benign]. Clinvar id is 1223010.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BCO1	NM_017429.3	c.193+272dup		intron_variant		ENST00000258168.7	NP_059125.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BCO1	ENST00000258168.7	c.193+272dup		intron_variant		1	NM_017429.3	ENSP00000258168	P1
BCO1	ENST00000564552.1	c.193+272dup		intron_variant		2		ENSP00000455219
BCO1	ENST00000563804.5	c.193+272dup		intron_variant, NMD_transcript_variant		2		ENSP00000457910

Frequencies

GnomAD3 genomes AF: 0.319 AC: 29695 AN: 93106 Hom.: 8564 Cov.: 0

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.333

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.319 AC: 29699 AN: 93132 Hom.: 8564 Cov.: 0 AF XY: 0.297 AC XY: 12342 AN XY: 41576

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.280

Gnomad4 ASJ AF: 0.436

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.368

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 20, 2021

- -

Computational scores

Source: dbNSFP v4.3

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: rs1176582576; hg19: chr16-81279454;