rs1554607553
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP3_StrongPP5
The NM_019098.5(CNGB3):āc.1751T>Cā(p.Leu584Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,826 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (no stars).
Frequency
Consequence
NM_019098.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CNGB3 | NM_019098.5 | c.1751T>C | p.Leu584Pro | missense_variant | 15/18 | ENST00000320005.6 | NP_061971.3 | |
CNGB3 | XM_011517138.3 | c.1337T>C | p.Leu446Pro | missense_variant | 13/16 | XP_011515440.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CNGB3 | ENST00000320005.6 | c.1751T>C | p.Leu584Pro | missense_variant | 15/18 | 1 | NM_019098.5 | ENSP00000316605.5 | ||
CNGB3 | ENST00000681546.1 | n.1571T>C | non_coding_transcript_exon_variant | 10/13 | ||||||
CNGB3 | ENST00000681746.1 | n.*162T>C | non_coding_transcript_exon_variant | 16/19 | ENSP00000505959.1 | |||||
CNGB3 | ENST00000681746.1 | n.*162T>C | 3_prime_UTR_variant | 16/19 | ENSP00000505959.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460826Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 726780
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Achromatopsia 3 Pathogenic:1
Likely 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