chr1-94077722-G-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1PM2PM5
The NM_000350.3(ABCA4):c.1522C>A(p.Arg508Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,461,636 control chromosomes in the GnomAD database, with no homozygous occurrence. 12/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R508C) has been classified as Likely pathogenic.
Frequency
Consequence
NM_000350.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCA4 | NM_000350.3 | c.1522C>A | p.Arg508Ser | missense_variant | 11/50 | ENST00000370225.4 | |
LOC124904222 | XR_007066231.1 | n.203-6007G>T | intron_variant, non_coding_transcript_variant | ||||
ABCA4 | XM_047416704.1 | c.1522C>A | p.Arg508Ser | missense_variant | 11/49 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCA4 | ENST00000370225.4 | c.1522C>A | p.Arg508Ser | missense_variant | 11/50 | 1 | NM_000350.3 | P1 | |
ABCA4 | ENST00000649773.1 | c.1522C>A | p.Arg508Ser | missense_variant | 11/19 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251082Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135686
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461636Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727060
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at