16-81245849-C-CT

Variant names:

• chr16-81245849-C-CT
• rs1176582576
• NM_017429.3:c.193+272dupT

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+272dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.32 (8564 hom., cov: 0)
• Consequence: BCO1 NM_017429.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.889
• 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-C-CT is Benign according to our data. Variant chr16-81245849-C-CT is described in ClinVar as Benign. ClinVar VariationId is 1223010.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.445 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+272dupT		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+246_193+247insT		intron	N/A	ENSP00000258168.2	Q9HAY6
	BCO1	ENST00000891666.1		c.193+246_193+247insT		intron	N/A	ENSP00000561725.1
	BCO1	ENST00000891665.1		c.193+246_193+247insT		intron	N/A	ENSP00000561724.1

Frequencies

GnomAD3 genomes AF: 0.319 AC: 29695 AN: 93106 Hom.: 8564 Cov.: 0

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.333

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.319 AC: 29699 AN: 93132 Hom.: 8564 Cov.: 0 AF XY: 0.297 AC XY: 12342 AN XY: 41576

African (AFR) AF: 0.101 AC: 2664 AN: 26420

American (AMR) AF: 0.280 AC: 1813 AN: 6474

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1189 AN: 2730

East Asian (EAS) AF: 0.154 AC: 420 AN: 2732

South Asian (SAS) AF: 0.229 AC: 473 AN: 2070

European-Finnish (FIN) AF: 0.143 AC: 192 AN: 1346

Middle Eastern (MID) AF: 0.340 AC: 36 AN: 106

European-Non Finnish (NFE) AF: 0.450 AC: 22192 AN: 49362

Other (OTH) AF: 0.368 AC: 444 AN: 1206

Alfa AF: 0.135 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		0.89
Mutation Taster		=100/0	polymorphism (auto)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1176582576; hg19: chr16-81279454;