chr16-57933314-T-C
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001297.5(CNGB1):c.1373-1436A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.771 in 152,204 control chromosomes in the GnomAD database, including 46,196 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.77 ( 46196 hom., cov: 33)
Consequence
CNGB1
NM_001297.5 intron
NM_001297.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0180
Publications
6 publications found
Genes affected
CNGB1 (HGNC:2151): (cyclic nucleotide gated channel subunit beta 1) In humans, the rod photoreceptor cGMP-gated cation channel helps regulate ion flow into the rod photoreceptor outer segment in response to light-induced alteration of the levels of intracellular cGMP. This channel consists of two subunits, alpha and beta, with the protein encoded by this gene representing the beta subunit. Defects in this gene are a cause of cause of retinitis pigmentosa type 45. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2013]
CNGB1 Gene-Disease associations (from GenCC):
- CNGB1-related retinopathyInheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
- retinitis pigmentosa 45Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
- retinitis pigmentosaInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CNGB1 | ENST00000251102.13 | c.1373-1436A>G | intron_variant | Intron 16 of 32 | 1 | NM_001297.5 | ENSP00000251102.8 | |||
CNGB1 | ENST00000564448.5 | c.1355-1436A>G | intron_variant | Intron 16 of 32 | 1 | ENSP00000454633.1 | ||||
CNGB1 | ENST00000564654.1 | c.224-1436A>G | intron_variant | Intron 4 of 4 | 4 | ENSP00000495566.1 | ||||
CNGB1 | ENST00000564450.1 | n.120+6116A>G | intron_variant | Intron 1 of 1 | 3 |
Frequencies
GnomAD3 genomes AF: 0.771 AC: 117286AN: 152084Hom.: 46132 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
117286
AN:
152084
Hom.:
Cov.:
33
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: 0.771 AC: 117412AN: 152204Hom.: 46196 Cov.: 33 AF XY: 0.770 AC XY: 57312AN XY: 74416 show subpopulations
GnomAD4 genome
AF:
AC:
117412
AN:
152204
Hom.:
Cov.:
33
AF XY:
AC XY:
57312
AN XY:
74416
show subpopulations
African (AFR)
AF:
AC:
39130
AN:
41556
American (AMR)
AF:
AC:
10552
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
AC:
2449
AN:
3470
East Asian (EAS)
AF:
AC:
3782
AN:
5174
South Asian (SAS)
AF:
AC:
3922
AN:
4822
European-Finnish (FIN)
AF:
AC:
7490
AN:
10592
Middle Eastern (MID)
AF:
AC:
209
AN:
292
European-Non Finnish (NFE)
AF:
AC:
47703
AN:
67986
Other (OTH)
AF:
AC:
1566
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1346
2692
4039
5385
6731
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
856
1712
2568
3424
4280
<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:
2834
AN:
3478
ClinVar
Not reported inComputational 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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