GeneBe

rs1176582576

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_017429.3(BCO1):​c.193+257_193+272delTTTTTTTTTTTTTTTT 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 0.000011 ( 0 hom., cov: 0)

Consequence

BCO1
NM_017429.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.96

Publications

0 publications found
Variant links:
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

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

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.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
BCO1
NM_017429.3
MANE Select
c.193+257_193+272delTTTTTTTTTTTTTTTT
intron
N/ANP_059125.2Q9HAY6

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
BCO1
ENST00000258168.7
TSL:1 MANE Select
c.193+247_193+262delTTTTTTTTTTTTTTTT
intron
N/AENSP00000258168.2Q9HAY6
BCO1
ENST00000891666.1
c.193+247_193+262delTTTTTTTTTTTTTTTT
intron
N/AENSP00000561725.1
BCO1
ENST00000891665.1
c.193+247_193+262delTTTTTTTTTTTTTTTT
intron
N/AENSP00000561724.1

Frequencies

GnomAD3 genomes
AF:
0.0000107
AC:
1
AN:
93368
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
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:
0.0000202
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0000107
AC:
1
AN:
93368
Hom.:
0
Cov.:
0
AF XY:
0.0000240
AC XY:
1
AN XY:
41680
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
26452
American (AMR)
AF:
0.00
AC:
0
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:
0.0000202
AC:
1
AN:
49474
Other (OTH)
AF:
0.00
AC:
0
AN:
1200
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.675
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

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

Publications

Other links and lift over

dbSNP: rs1176582576; hg19: chr16-81279454; API