16-81245849-CTTTTTTTTTTTTTTTT-CTTTTTTTT

Variant names:

• chr16-81245849-CTTTTTTTT-C
• rs1176582576
• NM_017429.3:c.193+265_193+272delTTTTTTTT

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_017429.3(BCO1):​c.193+265_193+272delTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.073 (464 hom., cov: 0)
• Consequence: BCO1 NM_017429.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.96
• Publications: 0 publications found

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]

BCO1 Gene-Disease associations (from GenCC):

• hereditary hypercarotenemia and vitamin A deficiency

  Inheritance: Unknown, AD Classification: SUPPORTIVE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Orphanet

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant 16-81245849-CTTTTTTTT-C is Benign according to our data. Variant chr16-81245849-CTTTTTTTT-C is described in ClinVar as Benign. ClinVar VariationId is 1222394.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017429.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCO1	NM_017429.3	MANE Select	c.193+265_193+272delTTTTTTTT		intron	N/A	NP_059125.2	Q9HAY6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCO1	ENST00000258168.7	TSL:1 MANE Select	c.193+247_193+254delTTTTTTTT		intron	N/A	ENSP00000258168.2	Q9HAY6
	BCO1	ENST00000891666.1		c.193+247_193+254delTTTTTTTT		intron	N/A	ENSP00000561725.1
	BCO1	ENST00000891665.1		c.193+247_193+254delTTTTTTTT		intron	N/A	ENSP00000561724.1

Frequencies

GnomAD3 genomes AF: 0.0727 AC: 6787 AN: 93330 Hom.: 464 Cov.: 0

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.00727

Gnomad AMR AF: 0.0511

Gnomad ASJ AF: 0.0267

Gnomad EAS AF: 0.000726

Gnomad SAS AF: 0.0448

Gnomad FIN AF: 0.0220

Gnomad MID AF: 0.0690

Gnomad NFE AF: 0.0257

Gnomad OTH AF: 0.0583

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

GnomAD4 genome AF: 0.0728 AC: 6795 AN: 93354 Hom.: 464 Cov.: 0 AF XY: 0.0738 AC XY: 3075 AN XY: 41680

African (AFR) AF: 0.186 AC: 4912 AN: 26442

American (AMR) AF: 0.0510 AC: 332 AN: 6516

Ashkenazi Jewish (ASJ) AF: 0.0267 AC: 73 AN: 2732

East Asian (EAS) AF: 0.000728 AC: 2 AN: 2746

South Asian (SAS) AF: 0.0452 AC: 94 AN: 2080

European-Finnish (FIN) AF: 0.0220 AC: 30 AN: 1362

Middle Eastern (MID) AF: 0.0741 AC: 8 AN: 108

European-Non Finnish (NFE) AF: 0.0257 AC: 1269 AN: 49470

Other (OTH) AF: 0.0579 AC: 70 AN: 1210

Alfa AF: 0.00827 Hom.: 177

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1176582576; hg19: chr16-81279454;