rs7743515
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001142800.2(EYS):c.2847-24C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.812 in 1,424,302 control chromosomes in the GnomAD database, including 470,811 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.83 ( 52440 hom., cov: 31)
Exomes 𝑓: 0.81 ( 418371 hom. )
Consequence
EYS
NM_001142800.2 intron
NM_001142800.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.904
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 -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
Variant 6-64886866-G-A is Benign according to our data. Variant chr6-64886866-G-A is described in ClinVar as [Benign]. Clinvar id is 1175362.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.837 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EYS | NM_001142800.2 | c.2847-24C>T | intron_variant | ENST00000503581.6 | |||
EYS | NM_001292009.2 | c.2847-24C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EYS | ENST00000503581.6 | c.2847-24C>T | intron_variant | 5 | NM_001142800.2 | A2 | |||
EYS | ENST00000370621.7 | c.2847-24C>T | intron_variant | 1 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.831 AC: 126094AN: 151762Hom.: 52399 Cov.: 31
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GnomAD3 exomes AF: 0.828 AC: 97661AN: 117980Hom.: 40481 AF XY: 0.824 AC XY: 51931AN XY: 63016
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GnomAD4 exome AF: 0.810 AC: 1031007AN: 1272422Hom.: 418371 Cov.: 20 AF XY: 0.811 AC XY: 510918AN XY: 630090
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GnomAD4 genome ? AF: 0.831 AC: 126193AN: 151880Hom.: 52440 Cov.: 31 AF XY: 0.833 AC XY: 61831AN XY: 74204
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Retinitis pigmentosa 25 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 01, 2021 | - - |
Computational scores
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Name
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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