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GeneBe

rs2033249

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001297.5(CNGB1):c.3462+203C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.381 in 151,912 control chromosomes in the GnomAD database, including 11,987 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 0.38 ( 11987 hom., cov: 32)

Consequence

CNGB1
NM_001297.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.430
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CNGB1NM_001297.5 linkuse as main transcriptc.3462+203C>T intron_variant ENST00000251102.13
CNGB1NM_001286130.2 linkuse as main transcriptc.3444+203C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CNGB1ENST00000251102.13 linkuse as main transcriptc.3462+203C>T intron_variant 1 NM_001297.5 P4Q14028-1
CNGB1ENST00000564448.5 linkuse as main transcriptc.3444+203C>T intron_variant 1 A2Q14028-4
CNGB1ENST00000565942.1 linkuse as main transcriptc.289-3195C>T intron_variant 5

Frequencies

GnomAD3 genomes
AF:
0.381
AC:
57896
AN:
151794
Hom.:
11984
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.225
Gnomad AMI
AF:
0.471
Gnomad AMR
AF:
0.355
Gnomad ASJ
AF:
0.572
Gnomad EAS
AF:
0.297
Gnomad SAS
AF:
0.411
Gnomad FIN
AF:
0.431
Gnomad MID
AF:
0.459
Gnomad NFE
AF:
0.467
Gnomad OTH
AF:
0.395
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.381
AC:
57916
AN:
151912
Hom.:
11987
Cov.:
32
AF XY:
0.379
AC XY:
28104
AN XY:
74224
show subpopulations
Gnomad4 AFR
AF:
0.225
Gnomad4 AMR
AF:
0.355
Gnomad4 ASJ
AF:
0.572
Gnomad4 EAS
AF:
0.297
Gnomad4 SAS
AF:
0.413
Gnomad4 FIN
AF:
0.431
Gnomad4 NFE
AF:
0.467
Gnomad4 OTH
AF:
0.391
Alfa
AF:
0.417
Hom.:
3473
Bravo
AF:
0.365
Asia WGS
AF:
0.330
AC:
1149
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
Cadd
Benign
0.032
Dann
Benign
0.85

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2033249; hg19: chr16-57921556; API