rs17479806
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001142800.2(EYS):c.5927+3413C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0251 in 151,960 control chromosomes in the GnomAD database, including 73 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.025 ( 73 hom., cov: 32)
Consequence
EYS
NM_001142800.2 intron
NM_001142800.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0940
Genes affected
EYS (HGNC:21555): (eyes shut homolog) The product of this gene contains multiple epidermal growth factor (EGF)-like and LamG domains. The protein is expressed in the photoreceptor layer of the retina, and the gene is mutated in autosomal recessive retinitis pigmentosa. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0251 (3811/151960) while in subpopulation NFE AF= 0.0377 (2561/67886). AF 95% confidence interval is 0.0365. There are 73 homozygotes in gnomad4. There are 1815 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 73 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EYS | NM_001142800.2 | c.5927+3413C>A | intron_variant | ENST00000503581.6 | |||
EYS | NM_001292009.2 | c.5927+3413C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EYS | ENST00000503581.6 | c.5927+3413C>A | intron_variant | 5 | NM_001142800.2 | A2 | |||
EYS | ENST00000370621.7 | c.5927+3413C>A | intron_variant | 1 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0251 AC: 3813AN: 151842Hom.: 73 Cov.: 32
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0251 AC: 3811AN: 151960Hom.: 73 Cov.: 32 AF XY: 0.0244 AC XY: 1815AN XY: 74298
GnomAD4 genome
?
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at