16-81245849-CTTTTTTTTTTTTTTTT-CTTT

Variant names:

• chr16-81245849-CTTTTTTTTTTTTT-C
• rs1176582576
• NM_017429.3:c.193+260_193+272delTTTTTTTTTTTTT

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_017429.3(BCO1):​c.193+260_193+272delTTTTTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.00040 (0 hom., cov: 0)
• Consequence: BCO1 NM_017429.3 intron
• Clinical Significance: Not reported in ClinVar
• 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: Likely_benign. The variant received -4 ACMG points.

• BS2: High AC in GnomAd4 at 37 Unknown,AD gene.

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+260_193+272delTTTTTTTTTTTTT		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+259delTTTTTTTTTTTTT		intron	N/A	ENSP00000258168.2	Q9HAY6
	BCO1	ENST00000891666.1		c.193+247_193+259delTTTTTTTTTTTTT		intron	N/A	ENSP00000561725.1
	BCO1	ENST00000891665.1		c.193+247_193+259delTTTTTTTTTTTTT		intron	N/A	ENSP00000561724.1

Frequencies

GnomAD3 genomes AF: 0.000396 AC: 37 AN: 93368 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000491

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000308

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000445

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.000396 AC: 37 AN: 93368 Hom.: 0 Cov.: 0 AF XY: 0.000432 AC XY: 18 AN XY: 41680

African (AFR) AF: 0.000491 AC: 13 AN: 26452

American (AMR) AF: 0.000308 AC: 2 AN: 6490

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2734

East Asian (EAS) AF: 0.00 AC: 0 AN: 2756

South Asian (SAS) AF: 0.00 AC: 0 AN: 2096

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1362

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 116

European-Non Finnish (NFE) AF: 0.000445 AC: 22 AN: 49474

Other (OTH) AF: 0.00 AC: 0 AN: 1200

Alfa AF: 0.00 Hom.: 177

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.0

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;