6-64912570-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001142800.2(EYS):c.2555T>C(p.Leu852Pro) variant causes a missense change. The variant allele was found at a frequency of 0.593 in 1,550,694 control chromosomes in the GnomAD database, including 276,892 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001142800.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
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EYS | ENST00000503581.6 | c.2555T>C | p.Leu852Pro | missense_variant | Exon 16 of 43 | 5 | NM_001142800.2 | ENSP00000424243.1 | ||
EYS | ENST00000370621.7 | c.2555T>C | p.Leu852Pro | missense_variant | Exon 16 of 44 | 1 | ENSP00000359655.3 |
Frequencies
GnomAD3 genomes AF: 0.664 AC: 100789AN: 151842Hom.: 34846 Cov.: 32
GnomAD3 exomes AF: 0.593 AC: 92797AN: 156496Hom.: 28224 AF XY: 0.586 AC XY: 48635AN XY: 82932
GnomAD4 exome AF: 0.585 AC: 818369AN: 1398734Hom.: 242008 Cov.: 42 AF XY: 0.583 AC XY: 402451AN XY: 689884
GnomAD4 genome AF: 0.664 AC: 100881AN: 151960Hom.: 34884 Cov.: 32 AF XY: 0.660 AC XY: 49037AN XY: 74258
ClinVar
Submissions by phenotype
Retinitis pigmentosa 25 Benign:5
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not specified Benign:3
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not provided Benign:2
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The variant is found in ARRP panel(s). -
Retinitis pigmentosa Benign:2
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This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Retinal dystrophy Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at