rs1385347376
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PVS1_ModeratePM2PP3_StrongPP5
The NM_019098.5(CNGB3):c.1056-2A>G variant causes a splice acceptor change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000138 in 1,454,088 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Pathogenic (no stars).
Frequency
Consequence
NM_019098.5 splice_acceptor
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CNGB3 | NM_019098.5 | c.1056-2A>G | splice_acceptor_variant | ENST00000320005.6 | |||
CNGB3 | XM_011517138.3 | c.642-2A>G | splice_acceptor_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNGB3 | ENST00000320005.6 | c.1056-2A>G | splice_acceptor_variant | 1 | NM_019098.5 | P1 | |||
CNGB3 | ENST00000681746.1 | c.1056-2A>G | splice_acceptor_variant, NMD_transcript_variant | ||||||
CNGB3 | ENST00000681546.1 | n.876-2A>G | splice_acceptor_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? Cov.: 30
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 250114Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135238
GnomAD4 exome AF: 0.00000138 AC: 2AN: 1454088Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 723518
GnomAD4 genome ? Cov.: 30
ClinVar
Submissions by phenotype
Achromatopsia 3 Pathogenic:1
Pathogenic, no assertion criteria provided | research | Molecular Genetics Laboratory, Institute for Ophthalmic Research | Mar 27, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at