chr6-64912769-G-C
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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.2382-26C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.592 in 1,299,052 control chromosomes in the GnomAD database, including 231,845 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.67 ( 35079 hom., cov: 32)
Exomes 𝑓: 0.58 ( 196766 hom. )
Consequence
EYS
NM_001142800.2 intron
NM_001142800.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.680
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=-0.86).
BP6
Variant 6-64912769-G-C is Benign according to our data. Variant chr6-64912769-G-C is described in ClinVar as [Benign]. Clinvar id is 1175365.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.665 AC: 101025AN: 151824Hom.: 35040 Cov.: 32
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GnomAD3 exomes AF: 0.592 AC: 28353AN: 47900Hom.: 8712 AF XY: 0.587 AC XY: 13822AN XY: 23534
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GnomAD4 exome AF: 0.582 AC: 667395AN: 1147108Hom.: 196766 Cov.: 20 AF XY: 0.581 AC XY: 318660AN XY: 548664
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GnomAD4 genome AF: 0.665 AC: 101118AN: 151944Hom.: 35079 Cov.: 32 AF XY: 0.662 AC XY: 49160AN XY: 74254
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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
Mar 03, 2015
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Retinitis pigmentosa 25 Benign:1
Jul 01, 2021
Genome-Nilou Lab
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
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Name
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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