ClinVar Miner

Submissions for variant NM_001297.5(CNGB1):c.3115G>A (p.Gly1039Arg)

gnomAD frequency: 0.00372  dbSNP: rs148999583
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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000177529 SCV000229412 likely benign not specified 2014-10-03 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000989610 SCV000398307 uncertain significance Retinitis pigmentosa 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
GeneDx RCV000761936 SCV000568998 uncertain significance not provided 2017-04-17 criteria provided, single submitter clinical testing The c.3115 G>A variant in the CNGB1 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.3115 G>A variant is observed in 301/66256 (0.45%) alleles from individuals of European background, including one homozygous individual, in the ExAC dataset (Lek et al., 2016). In-silico splice models predict that c.3115 G>A may create a cryptic splice acceptor site that could supplant the natural splice acceptor site. However, in the absence of RNA/functional studies, the actual effect of the c.3115 G>A change in this individual is unknown. If c.3115 G>A does not alter splicing, it will result in the G1039R missense change. The G1039R variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. We interpret c.3115 G>A as a variant of uncertain significance.
CeGaT Center for Human Genetics Tuebingen RCV000761936 SCV000892163 uncertain significance not provided 2018-06-01 criteria provided, single submitter clinical testing
Mendelics RCV000989610 SCV001140116 likely benign Retinitis pigmentosa 2019-05-28 criteria provided, single submitter clinical testing
Invitae RCV000761936 SCV001646495 likely benign not provided 2024-01-31 criteria provided, single submitter clinical testing
Ambry Genetics RCV002517713 SCV003684196 uncertain significance Inborn genetic diseases 2021-09-16 criteria provided, single submitter clinical testing The c.3115G>A (p.G1039R) alteration is located in exon 31 (coding exon 30) of the CNGB1 gene. This alteration results from a G to A substitution at nucleotide position 3115, causing the glycine (G) at amino acid position 1039 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
PreventionGenetics, part of Exact Sciences RCV003937605 SCV004753769 likely benign CNGB1-related disorder 2019-09-12 criteria provided, single submitter clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
Clinical Genetics, Academic Medical Center RCV000761936 SCV001920349 likely benign not provided no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000761936 SCV001968023 likely benign not provided no assertion criteria provided clinical testing

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