rs7184838

Variant summary

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

The NM_001297.5(CNGB1):​c.1643+946C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,050 control chromosomes in the GnomAD database, including 2,225 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 0.10 ( 2225 hom., cov: 31)

Consequence

CNGB1
NM_001297.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.25
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=-0.95).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CNGB1NM_001297.5 linkc.1643+946C>T intron_variant Intron 18 of 32 ENST00000251102.13 NP_001288.3 Q14028-1
CNGB1NM_001286130.2 linkc.1625+946C>T intron_variant Intron 18 of 32 NP_001273059.1 Q14028-4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CNGB1ENST00000251102.13 linkc.1643+946C>T intron_variant Intron 18 of 32 1 NM_001297.5 ENSP00000251102.8 Q14028-1
CNGB1ENST00000564448.5 linkc.1625+946C>T intron_variant Intron 18 of 32 1 ENSP00000454633.1 Q14028-4

Frequencies

GnomAD3 genomes
AF:
0.100
AC:
15245
AN:
151934
Hom.:
2215
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.320
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0471
Gnomad ASJ
AF:
0.0291
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00663
Gnomad FIN
AF:
0.00245
Gnomad MID
AF:
0.0411
Gnomad NFE
AF:
0.0148
Gnomad OTH
AF:
0.0588
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.101
AC:
15287
AN:
152050
Hom.:
2225
Cov.:
31
AF XY:
0.0977
AC XY:
7265
AN XY:
74344
show subpopulations
Gnomad4 AFR
AF:
0.321
Gnomad4 AMR
AF:
0.0469
Gnomad4 ASJ
AF:
0.0291
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00663
Gnomad4 FIN
AF:
0.00245
Gnomad4 NFE
AF:
0.0148
Gnomad4 OTH
AF:
0.0582
Alfa
AF:
0.0211
Hom.:
43
Bravo
AF:
0.114
Asia WGS
AF:
0.0230
AC:
82
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
0.26
DANN
Benign
0.53

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: rs7184838; hg19: chr16-57956231; API