16-81239023-T-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+51T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0251 in 1,415,534 control chromosomes in the GnomAD database, including 287 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.036 (103 hom., cov: 30)
  • Exomes 𝑓: 0.024 (184 hom.)
• Consequence: BCO1 NM_017429.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.214

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=-0.9).
• BP6: Variant 16-81239023-T-A is Benign according to our data. Variant chr16-81239023-T-A is described in ClinVar as [Benign]. Clinvar id is 1267670.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BCO1	NM_017429.3	c.64+51T>A		intron_variant		ENST00000258168.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCO1	ENST00000258168.7	c.64+51T>A		intron_variant		1	NM_017429.3	P1
BCO1	ENST00000564552.1	c.64+51T>A		intron_variant		2
BCO1	ENST00000563804.5	c.64+51T>A		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0363 AC: 5068 AN: 139450 Hom.: 103 Cov.: 30

Gnomad AFR AF: 0.0780

Gnomad AMI AF: 0.00552

Gnomad AMR AF: 0.0230

Gnomad ASJ AF: 0.0375

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.0287

Gnomad FIN AF: 0.0402

Gnomad MID AF: 0.0397

Gnomad NFE AF: 0.0230

Gnomad OTH AF: 0.0300

GnomAD3 exomes AF: 0.0326 AC: 4826 AN: 147846 Hom.: 44 AF XY: 0.0327 AC XY: 2713 AN XY: 82856

Gnomad AFR exome AF: 0.0991

Gnomad AMR exome AF: 0.0171

Gnomad ASJ exome AF: 0.0374

Gnomad EAS exome AF: 0.000470

Gnomad SAS exome AF: 0.0367

Gnomad FIN exome AF: 0.0481

Gnomad NFE exome AF: 0.0289

Gnomad OTH exome AF: 0.0376

GnomAD4 exome AF: 0.0239 AC: 30501 AN: 1276042 Hom.: 184 Cov.: 22 AF XY: 0.0244 AC XY: 15527 AN XY: 635868

Gnomad4 AFR exome AF: 0.0682

Gnomad4 AMR exome AF: 0.0138

Gnomad4 ASJ exome AF: 0.0331

Gnomad4 EAS exome AF: 0.000360

Gnomad4 SAS exome AF: 0.0306

Gnomad4 FIN exome AF: 0.0395

Gnomad4 NFE exome AF: 0.0223

Gnomad4 OTH exome AF: 0.0268

GnomAD4 genome AF: 0.0364 AC: 5078 AN: 139492 Hom.: 103 Cov.: 30 AF XY: 0.0353 AC XY: 2409 AN XY: 68278

Gnomad4 AFR AF: 0.0782

Gnomad4 AMR AF: 0.0229

Gnomad4 ASJ AF: 0.0375

Gnomad4 EAS AF: 0.00194

Gnomad4 SAS AF: 0.0285

Gnomad4 FIN AF: 0.0402

Gnomad4 NFE AF: 0.0230

Gnomad4 OTH AF: 0.0297

Alfa AF: 0.00975 Hom.: 2

Bravo AF: 0.0341

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

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.88
Dann	Benign	0.17

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: rs58067823; hg19: chr16-81272628;