chr16-57917490-T-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001297.5(CNGB1):c.1958-14A>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 1,612,868 control chromosomes in the GnomAD database, including 58,880 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.30 ( 7595 hom., cov: 31)
Exomes 𝑓: 0.26 ( 51285 hom. )
Consequence
CNGB1
NM_001297.5 splice_polypyrimidine_tract, intron
NM_001297.5 splice_polypyrimidine_tract, intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.25
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 -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
?
Variant 16-57917490-T-G is Benign according to our data. Variant chr16-57917490-T-G is described in ClinVar as [Benign]. Clinvar id is 257960.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-57917490-T-G is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CNGB1 | NM_001297.5 | c.1958-14A>C | splice_polypyrimidine_tract_variant, intron_variant | ENST00000251102.13 | |||
CNGB1 | NM_001286130.2 | c.1940-14A>C | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNGB1 | ENST00000251102.13 | c.1958-14A>C | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001297.5 | P4 | |||
CNGB1 | ENST00000564448.5 | c.1940-14A>C | splice_polypyrimidine_tract_variant, intron_variant | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.304 AC: 46141AN: 151748Hom.: 7580 Cov.: 31
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GnomAD3 exomes AF: 0.271 AC: 67551AN: 248924Hom.: 9836 AF XY: 0.274 AC XY: 37005AN XY: 135114
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GnomAD4 exome AF: 0.261 AC: 380651AN: 1461000Hom.: 51285 Cov.: 35 AF XY: 0.263 AC XY: 190952AN XY: 726866
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GnomAD4 genome ? AF: 0.304 AC: 46199AN: 151868Hom.: 7595 Cov.: 31 AF XY: 0.304 AC XY: 22562AN XY: 74232
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ClinVar
Significance: Benign
Submissions summary: Benign:7
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:4
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Apr 14, 2016 | - - |
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 03, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Retinitis pigmentosa Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | 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 and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at