chr16-57933314-T-C

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0180

Publications

6 publications found
Variant links:
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 retinopathy
    Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
  • retinitis pigmentosa 45
    Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
  • retinitis pigmentosa
    Inheritance: 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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CNGB1NM_001297.5 linkc.1373-1436A>G intron_variant Intron 16 of 32 ENST00000251102.13 NP_001288.3 Q14028-1
CNGB1NM_001286130.2 linkc.1355-1436A>G intron_variant Intron 16 of 32 NP_001273059.1 Q14028-4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CNGB1ENST00000251102.13 linkc.1373-1436A>G intron_variant Intron 16 of 32 1 NM_001297.5 ENSP00000251102.8 Q14028-1
CNGB1ENST00000564448.5 linkc.1355-1436A>G intron_variant Intron 16 of 32 1 ENSP00000454633.1 Q14028-4
CNGB1ENST00000564654.1 linkc.224-1436A>G intron_variant Intron 4 of 4 4 ENSP00000495566.1 A0A2R8Y6Y0
CNGB1ENST00000564450.1 linkn.120+6116A>G intron_variant Intron 1 of 1 3

Frequencies

GnomAD3 genomes
AF:
0.771
AC:
117286
AN:
152084
Hom.:
46132
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.941
Gnomad AMI
AF:
0.669
Gnomad AMR
AF:
0.690
Gnomad ASJ
AF:
0.706
Gnomad EAS
AF:
0.731
Gnomad SAS
AF:
0.814
Gnomad FIN
AF:
0.707
Gnomad MID
AF:
0.710
Gnomad NFE
AF:
0.702
Gnomad OTH
AF:
0.739
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.771
AC:
117412
AN:
152204
Hom.:
46196
Cov.:
33
AF XY:
0.770
AC XY:
57312
AN XY:
74416
show subpopulations
African (AFR)
AF:
0.942
AC:
39130
AN:
41556
American (AMR)
AF:
0.690
AC:
10552
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
0.706
AC:
2449
AN:
3470
East Asian (EAS)
AF:
0.731
AC:
3782
AN:
5174
South Asian (SAS)
AF:
0.813
AC:
3922
AN:
4822
European-Finnish (FIN)
AF:
0.707
AC:
7490
AN:
10592
Middle Eastern (MID)
AF:
0.716
AC:
209
AN:
292
European-Non Finnish (NFE)
AF:
0.702
AC:
47703
AN:
67986
Other (OTH)
AF:
0.741
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:
0.719
Hom.:
78330
Bravo
AF:
0.773
Asia WGS
AF:
0.815
AC:
2834
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
4.9
DANN
Benign
0.74
PhyloP100
-0.018
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

Publications

Other links and lift over

dbSNP: rs247052; hg19: chr16-57967218; API