16-81245849-CTTTTTT-C

Position:

• chr16-81245849-CTTTTTT-C

Variant summary

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

The NM_017429.3(BCO1):​c.193+267_193+272del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.34 (4982 hom., cov: 0)
• Consequence: BCO1 NM_017429.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.96

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-CTTTTTT-C is Benign according to our data. Variant chr16-81245849-CTTTTTT-C is described in ClinVar as [Benign]. Clinvar id is 1246078.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BCO1	NM_017429.3	c.193+267_193+272del		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+267_193+272del		intron_variant		1	NM_017429.3	ENSP00000258168	P1
BCO1	ENST00000564552.1	c.193+267_193+272del		intron_variant		2		ENSP00000455219
BCO1	ENST00000563804.5	c.193+267_193+272del		intron_variant, NMD_transcript_variant		2		ENSP00000457910

Frequencies

GnomAD3 genomes AF: 0.341 AC: 31638 AN: 92814 Hom.: 4984 Cov.: 0

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.407

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.341 AC: 31639 AN: 92838 Hom.: 4982 Cov.: 0 AF XY: 0.345 AC XY: 14281 AN XY: 41420

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.430

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.329

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 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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;