rs66502009
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001142800.2(EYS):c.6834+61T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 1,027,904 control chromosomes in the GnomAD database, including 71,488 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.30 ( 7796 hom., cov: 31)
Exomes 𝑓: 0.38 ( 63692 hom. )
Consequence
EYS
NM_001142800.2 intron
NM_001142800.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.422
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=-0.8).
BP6
?
Variant 6-63999014-A-C is Benign according to our data. Variant chr6-63999014-A-C is described in ClinVar as [Benign]. Clinvar id is 1175356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EYS | NM_001142800.2 | c.6834+61T>G | intron_variant | ENST00000503581.6 | |||
LOC107986608 | XR_007059629.1 | n.317-22373A>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EYS | ENST00000503581.6 | c.6834+61T>G | intron_variant | 5 | NM_001142800.2 | A2 | |||
EYS | ENST00000370621.7 | c.6834+61T>G | intron_variant | 1 | P2 | ||||
EYS | ENST00000398580.3 | c.148+61T>G | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.301 AC: 45781AN: 151904Hom.: 7797 Cov.: 31
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GnomAD4 exome AF: 0.375 AC: 328599AN: 875882Hom.: 63692 AF XY: 0.379 AC XY: 170786AN XY: 450548
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GnomAD4 genome ? AF: 0.301 AC: 45788AN: 152022Hom.: 7796 Cov.: 31 AF XY: 0.299 AC XY: 22221AN XY: 74282
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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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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at