16-81245877-T-C

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.193+274T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.41 (10546 hom., cov: 19)
• Consequence: BCO1 NM_017429.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.50

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=-1.01).
• BP6: Variant 16-81245877-T-C is Benign according to our data. Variant chr16-81245877-T-C is described in ClinVar as [Benign]. Clinvar id is 1257454.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BCO1	NM_017429.3	c.193+274T>C		intron_variant		ENST00000258168.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCO1	ENST00000258168.7	c.193+274T>C		intron_variant		1	NM_017429.3	P1
BCO1	ENST00000564552.1	c.193+274T>C		intron_variant		2
BCO1	ENST00000563804.5	c.193+274T>C		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.406 AC: 50386 AN: 124234 Hom.: 10534 Cov.: 19

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.406 AC: 50405 AN: 124278 Hom.: 10546 Cov.: 19 AF XY: 0.403 AC XY: 23734 AN XY: 58940

Gnomad4 AFR AF: 0.527

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.360

Gnomad4 OTH AF: 0.360

Alfa AF: 0.378 Hom.: 923

Bravo AF: 0.388

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

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.93
Dann	Benign	0.30

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: rs11646549; hg19: chr16-81279482;