chr6-65295995-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001142800.2(EYS):c.1891G>A(p.Gly631Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 1,550,630 control chromosomes in the GnomAD database, including 271,627 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 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.1891G>A | p.Gly631Ser | missense_variant | Exon 12 of 43 | 5 | NM_001142800.2 | ENSP00000424243.1 | ||
EYS | ENST00000370621.7 | c.1891G>A | p.Gly631Ser | missense_variant | Exon 12 of 44 | 1 | ENSP00000359655.3 | |||
EYS | ENST00000370615.3 | n.329G>A | non_coding_transcript_exon_variant | Exon 2 of 2 | 3 | |||||
EYS | ENST00000447127.1 | n.347G>A | non_coding_transcript_exon_variant | Exon 3 of 3 | 4 |
Frequencies
GnomAD3 genomes AF: 0.520 AC: 78876AN: 151592Hom.: 22751 Cov.: 32
GnomAD3 exomes AF: 0.625 AC: 98325AN: 157416Hom.: 32264 AF XY: 0.625 AC XY: 51904AN XY: 83060
GnomAD4 exome AF: 0.591 AC: 826335AN: 1398920Hom.: 248862 Cov.: 56 AF XY: 0.593 AC XY: 409393AN XY: 689948
GnomAD4 genome AF: 0.520 AC: 78910AN: 151710Hom.: 22765 Cov.: 32 AF XY: 0.527 AC XY: 39084AN XY: 74156
ClinVar
Submissions by phenotype
not specified Benign:4
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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Retinitis pigmentosa 25 Benign:4
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Retinitis pigmentosa Benign:2
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. -
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not provided Benign:1
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Retinal dystrophy Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at