1-94051698-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PM5PP3_ModeratePP5
The NM_000350.3(ABCA4):c.2588G>A(p.Gly863Glu) variant causes a missense, splice region change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in Lovd as Likely pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G863A) has been classified as Likely pathogenic.
Frequency
Consequence
NM_000350.3 missense, splice_region
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 |
---|---|---|---|---|---|---|---|
ABCA4 | NM_000350.3 | c.2588G>A | p.Gly863Glu | missense_variant, splice_region_variant | 17/50 | ENST00000370225.4 | |
ABCA4 | XM_047416704.1 | c.2366G>A | p.Gly789Glu | missense_variant, splice_region_variant | 16/49 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCA4 | ENST00000370225.4 | c.2588G>A | p.Gly863Glu | missense_variant, splice_region_variant | 17/50 | 1 | NM_000350.3 | P1 | |
ABCA4 | ENST00000649773.1 | c.2366G>A | p.Gly789Glu | missense_variant, splice_region_variant | 16/19 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251244Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135782
GnomAD4 exome Cov.: 30
GnomAD4 genome ? Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at