6-63721512-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM1PM2BP4
The NM_001142800.2(EYS):c.8519A>G(p.Glu2840Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. E2840E) has been classified as Likely benign.
Frequency
Consequence
NM_001142800.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EYS | NM_001142800.2 | c.8519A>G | p.Glu2840Gly | missense_variant | 43/43 | ENST00000503581.6 | |
PHF3 | NM_001370348.2 | c.*7804T>C | 3_prime_UTR_variant | 16/16 | ENST00000262043.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EYS | ENST00000503581.6 | c.8519A>G | p.Glu2840Gly | missense_variant | 43/43 | 5 | NM_001142800.2 | A2 | |
EYS | ENST00000370621.7 | c.8582A>G | p.Glu2861Gly | missense_variant | 44/44 | 1 | P2 | ||
PHF3 | ENST00000262043.8 | c.*7804T>C | 3_prime_UTR_variant | 16/16 | 5 | NM_001370348.2 | P1 | ||
PHF3 | ENST00000505138.1 | c.363+10150T>C | intron_variant | 3 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Color vision defect;C0271385:Horizontal nystagmus;C0854723:Retinal dystrophy;C3665347:Visual impairment Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Centre for Mendelian Genomics, University Medical Centre Ljubljana | Jan 01, 2017 | - - |
Astigmatism;C0024440:Cystoid macular edema;C0476397:Abnormal electroretinogram;C0858618:Dyschromatopsia;C1862475:Abnormality of retinal pigmentation;C4021561:Electronegative electroretinogram;C4551715:Pigmentary retinopathy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Centre for Mendelian Genomics, University Medical Centre Ljubljana | Jan 01, 2017 | - - |
Retinitis pigmentosa 25 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Centre for Mendelian Genomics, University Medical Centre Ljubljana | Jan 01, 2016 | This variant was classified as: Uncertain significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at