rs75861378
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_019098.5(CNGB3):c.853-45T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00237 in 1,290,418 control chromosomes in the GnomAD database, including 57 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.011 ( 31 hom., cov: 32)
Exomes 𝑓: 0.0012 ( 26 hom. )
Consequence
CNGB3
NM_019098.5 intron
NM_019098.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.825
Genes affected
CNGB3 (HGNC:2153): (cyclic nucleotide gated channel subunit beta 3) This gene encodes the beta subunit of a cyclic nucleotide-gated ion channel. The encoded beta subunit appears to play a role in modulation of channel function in cone photoreceptors. This heterotetrameric channel is necessary for sensory transduction, and mutations in this gene have been associated with achromatopsia 3, progressive cone dystrophy, and juvenile macular degeneration, also known as Stargardt Disease. [provided by RefSeq, Feb 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
?
Variant 8-86654107-A-G is Benign according to our data. Variant chr8-86654107-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 261091.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0113 (1721/152222) while in subpopulation AFR AF= 0.0392 (1629/41536). AF 95% confidence interval is 0.0376. There are 31 homozygotes in gnomad4. There are 821 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 31 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CNGB3 | NM_019098.5 | c.853-45T>C | intron_variant | ENST00000320005.6 | |||
CNGB3 | XM_011517138.3 | c.439-45T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNGB3 | ENST00000320005.6 | c.853-45T>C | intron_variant | 1 | NM_019098.5 | P1 | |||
CNGB3 | ENST00000681746.1 | c.853-45T>C | intron_variant, NMD_transcript_variant | ||||||
CNGB3 | ENST00000681546.1 | n.673-45T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0113 AC: 1722AN: 152104Hom.: 31 Cov.: 32
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GnomAD3 exomes AF: 0.00290 AC: 719AN: 247754Hom.: 8 AF XY: 0.00213 AC XY: 285AN XY: 134064
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GnomAD4 exome AF: 0.00117 AC: 1334AN: 1138196Hom.: 26 Cov.: 16 AF XY: 0.00100 AC XY: 582AN XY: 581862
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GnomAD4 genome ? AF: 0.0113 AC: 1721AN: 152222Hom.: 31 Cov.: 32 AF XY: 0.0110 AC XY: 821AN XY: 74426
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at