rs61753021
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM1PM2PM5PP3_StrongPP5_Moderate
The NM_000350.3(ABCA4):c.5114G>T(p.Arg1705Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,132 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 Likely pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1705Q) has been classified as Likely pathogenic.
Frequency
Consequence
NM_000350.3 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 |
---|---|---|---|---|---|---|---|
ABCA4 | NM_000350.3 | c.5114G>T | p.Arg1705Leu | missense_variant | 36/50 | ENST00000370225.4 | |
ABCA4 | XM_047416704.1 | c.4892G>T | p.Arg1631Leu | missense_variant | 35/49 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCA4 | ENST00000370225.4 | c.5114G>T | p.Arg1705Leu | missense_variant | 36/50 | 1 | NM_000350.3 | P1 | |
ABCA4 | ENST00000460514.1 | n.608G>T | non_coding_transcript_exon_variant | 7/7 | 5 | ||||
ABCA4 | ENST00000470771.1 | n.224G>T | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000801 AC: 2AN: 249646Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134862
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461132Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 726714
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Severe early-childhood-onset retinal dystrophy Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Institute of Human Genetics, Univ. Regensburg, Univ. Regensburg | Jan 01, 2016 | - - |
not provided Other:1
not provided, no classification provided | literature only | Retina International | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at