rs104893612
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM1PM2PM5PP3_StrongPP5_Moderate
The NM_001298.3(CNGA3):c.488C>T(p.Pro163Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000991 in 1,613,734 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P163Q) has been classified as Likely pathogenic.
Frequency
Consequence
NM_001298.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CNGA3 | NM_001298.3 | c.488C>T | p.Pro163Leu | missense_variant | 6/8 | ENST00000272602.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNGA3 | ENST00000272602.7 | c.488C>T | p.Pro163Leu | missense_variant | 6/8 | 1 | NM_001298.3 | A1 | |
CNGA3 | ENST00000436404.6 | c.434C>T | p.Pro145Leu | missense_variant | 5/7 | 1 | P4 | ||
CNGA3 | ENST00000393503.2 | n.493C>T | non_coding_transcript_exon_variant | 2/2 | 4 | ||||
CNGA3 | ENST00000409937.1 | n.641C>T | non_coding_transcript_exon_variant | 6/8 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152246Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251488Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135918
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461488Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727052
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152246Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74374
ClinVar
Submissions by phenotype
Achromatopsia 2 Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | Palindrome, Gene Kavoshgaran Aria | Feb 29, 2024 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 01, 1998 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at