rs1555493707

Variant names:

• chr16-57959886-A-T
• rs1555493707
• NM_001297.5:c.761+2T>A

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1 PM2 PP5

The NM_001297.5(CNGB1):​c.761+2T>A variant causes a splice donor, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (no stars).

• Frequency: Genomes: not found (cov: 32)
• Consequence: CNGB1 NM_001297.5 splice_donor, intron
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Likely pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 3.52

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]

ACMG classification

Verdict is Pathogenic. Variant got 11 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, LoF is a know mechanism of disease, No cryptic splice site detected. Exon removal results in frameshift change.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 16-57959886-A-T is Pathogenic according to our data. Variant chr16-57959886-A-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 437978.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr16-57959886-A-T is described in Lovd as [Likely_pathogenic]. Variant chr16-57959886-A-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNGB1	NM_001297.5	c.761+2T>A		splice_donor_variant, intron_variant	Intron 10 of 32	ENST00000251102.13	NP_001288.3
CNGB1	NM_001286130.2	c.743+2T>A		splice_donor_variant, intron_variant	Intron 10 of 32		NP_001273059.1
CNGB1	NM_001135639.2	c.761+2T>A		splice_donor_variant, intron_variant	Intron 10 of 12		NP_001129111.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNGB1	ENST00000251102.13	c.761+2T>A		splice_donor_variant, intron_variant	Intron 10 of 32	1	NM_001297.5	ENSP00000251102.8
CNGB1	ENST00000564448.5	c.743+2T>A		splice_donor_variant, intron_variant	Intron 10 of 32	1		ENSP00000454633.1
CNGB1	ENST00000311183.8	c.761+2T>A		splice_donor_variant, intron_variant	Intron 10 of 12	1		ENSP00000311670.4
CNGB1	ENST00000562761.1	c.*120T>A		downstream_gene_variant		3		ENSP00000455708.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Retinitis pigmentosa Pathogenic:1

Jan 01, 2015

NIHR Bioresource Rare Diseases, University of Cambridge

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: research

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Benign	-0.23
CADD	Pathogenic	28
DANN	Benign	0.96
Eigen	Pathogenic	0.68
Eigen_PC	Uncertain	0.41
FATHMM_MKL	Uncertain	0.91	D
GERP RS		2.8

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.95
SpliceAI score (max)		0.97		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.97		Position offset: 2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1555493707; hg19: chr16-57993790;