chr16-81260064-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_017429.3(BCO1):c.323+259G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.031 in 152,212 control chromosomes in the GnomAD database, including 217 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.031 ( 217 hom., cov: 32)
Consequence
BCO1
NM_017429.3 intron
NM_017429.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.108
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 deficiencyInheritance: Unknown, AD Classification: SUPPORTIVE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
Variant 16-81260064-G-A is Benign according to our data. Variant chr16-81260064-G-A is described in ClinVar as [Benign]. Clinvar id is 1244506.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BCO1 | ENST00000258168.7 | c.323+259G>A | intron_variant | Intron 3 of 10 | 1 | NM_017429.3 | ENSP00000258168.2 | |||
BCO1 | ENST00000564552.1 | c.323+259G>A | intron_variant | Intron 3 of 3 | 2 | ENSP00000455219.1 | ||||
BCO1 | ENST00000563804.5 | n.194-2072G>A | intron_variant | Intron 2 of 9 | 2 | ENSP00000457910.1 |
Frequencies
GnomAD3 genomes AF: 0.0309 AC: 4696AN: 152094Hom.: 215 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
4696
AN:
152094
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0310 AC: 4716AN: 152212Hom.: 217 Cov.: 32 AF XY: 0.0297 AC XY: 2209AN XY: 74410 show subpopulations
GnomAD4 genome
AF:
AC:
4716
AN:
152212
Hom.:
Cov.:
32
AF XY:
AC XY:
2209
AN XY:
74410
show subpopulations
African (AFR)
AF:
AC:
4435
AN:
41512
American (AMR)
AF:
AC:
151
AN:
15272
Ashkenazi Jewish (ASJ)
AF:
AC:
33
AN:
3468
East Asian (EAS)
AF:
AC:
0
AN:
5188
South Asian (SAS)
AF:
AC:
4
AN:
4822
European-Finnish (FIN)
AF:
AC:
5
AN:
10596
Middle Eastern (MID)
AF:
AC:
1
AN:
294
European-Non Finnish (NFE)
AF:
AC:
45
AN:
68036
Other (OTH)
AF:
AC:
42
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
208
416
624
832
1040
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
50
100
150
200
250
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
23
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jun 19, 2021
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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