rs9453276
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001142800.2(EYS):c.1300-9316T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.674 in 151,936 control chromosomes in the GnomAD database, including 34,602 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 0.67 ( 34602 hom., cov: 32)
Consequence
EYS
NM_001142800.2 intron
NM_001142800.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.167
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=-0.98).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EYS | NM_001142800.2 | c.1300-9316T>C | intron_variant | ENST00000503581.6 | |||
EYS | NM_001142801.2 | c.1300-9316T>C | intron_variant | ||||
EYS | NM_001292009.2 | c.1300-9316T>C | intron_variant | ||||
EYS | NM_198283.2 | c.1300-9316T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EYS | ENST00000503581.6 | c.1300-9316T>C | intron_variant | 5 | NM_001142800.2 | A2 | |||
EYS | ENST00000342421.9 | c.1300-9316T>C | intron_variant | 1 | |||||
EYS | ENST00000370621.7 | c.1300-9316T>C | intron_variant | 1 | P2 | ||||
EYS | ENST00000393380.6 | c.1300-9316T>C | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.674 AC: 102334AN: 151818Hom.: 34589 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: 0.674 AC: 102389AN: 151936Hom.: 34602 Cov.: 32 AF XY: 0.672 AC XY: 49889AN XY: 74248
GnomAD4 genome
?
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102389
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32
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49889
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74248
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2237
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3474
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