6-63720598-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001142800.2(EYS):c.9433T>G(p.Ter3145GluextTer12) variant causes a stop lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000204 in 1,470,844 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. *3145*) has been classified as Likely benign.
Frequency
Consequence
NM_001142800.2 stop_lost
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EYS | NM_001142800.2 | c.9433T>G | p.Ter3145GluextTer12 | stop_lost | 43/43 | ENST00000503581.6 | |
PHF3 | NM_001370348.2 | c.*6890A>C | 3_prime_UTR_variant | 16/16 | ENST00000262043.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EYS | ENST00000503581.6 | c.9433T>G | p.Ter3145GluextTer12 | stop_lost | 43/43 | 5 | NM_001142800.2 | A2 | |
EYS | ENST00000370621.7 | c.9496T>G | p.Ter3166GluextTer12 | stop_lost | 44/44 | 1 | P2 | ||
PHF3 | ENST00000262043.8 | c.*6890A>C | 3_prime_UTR_variant | 16/16 | 5 | NM_001370348.2 | P1 | ||
PHF3 | ENST00000505138.1 | c.363+9236A>C | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152154Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000152 AC: 2AN: 1318690Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0AN XY: 645050
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74330
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 10, 2022 | This sequence change disrupts the translational stop signal of the EYS mRNA. It is expected to extend the length of the EYS protein by 12 additional amino acid residues. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with EYS-related conditions. ClinVar contains an entry for this variant (Variation ID: 1519786). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at