rs886044747
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_000350.3(ABCA4):c.5189G>A(p.Trp1730Ter) variant causes a stop gained change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000138 in 1,453,330 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 (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_000350.3 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCA4 | NM_000350.3 | c.5189G>A | p.Trp1730Ter | stop_gained | 36/50 | ENST00000370225.4 | |
ABCA4 | XM_047416704.1 | c.4967G>A | p.Trp1656Ter | stop_gained | 35/49 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCA4 | ENST00000370225.4 | c.5189G>A | p.Trp1730Ter | stop_gained | 36/50 | 1 | NM_000350.3 | P1 | |
ABCA4 | ENST00000460514.1 | n.683G>A | non_coding_transcript_exon_variant | 7/7 | 5 | ||||
ABCA4 | ENST00000470771.1 | n.299G>A | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000421 AC: 1AN: 237330Hom.: 0 AF XY: 0.00000783 AC XY: 1AN XY: 127718
GnomAD4 exome AF: 0.00000138 AC: 2AN: 1453330Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 721880
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Severe early-childhood-onset retinal dystrophy Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing;in vitro | Institute of Human Genetics, Univ. Regensburg, Univ. Regensburg | Jan 01, 2016 | - - |
Retinal dystrophy Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Blueprint Genetics | Aug 06, 2018 | - - |
Stargardt disease Pathogenic:1
Pathogenic, no assertion criteria provided | research | Sharon lab, Hadassah-Hebrew University Medical Center | Jun 23, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at