rs1060499536
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PVS1_ModeratePM2PP5
The NM_000440.3(PDE6A):c.1408-2A>G variant causes a splice acceptor, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000684 in 1,461,834 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_000440.3 splice_acceptor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PDE6A | ENST00000255266.10 | c.1408-2A>G | splice_acceptor_variant, intron_variant | 1 | NM_000440.3 | ENSP00000255266.5 | ||||
PDE6A | ENST00000508173.5 | n.1384-2A>G | splice_acceptor_variant, intron_variant | 1 | ||||||
PDE6A | ENST00000613228.1 | c.1165-2A>G | splice_acceptor_variant, intron_variant | 5 | ENSP00000478060.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251428Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135894
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461834Hom.: 0 Cov.: 35 AF XY: 0.0000124 AC XY: 9AN XY: 727226
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Retinitis pigmentosa 43 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 07, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at