7-148829754-T-C
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PM5PP2PP3_Moderate
The NM_004456.5(EZH2):āc.458A>Gā(p.Tyr153Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000686 in 1,458,404 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as not provided (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Y153H) has been classified as Likely pathogenic.
Frequency
Consequence
NM_004456.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EZH2 | NM_004456.5 | c.458A>G | p.Tyr153Cys | missense_variant | 5/20 | ENST00000320356.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EZH2 | ENST00000320356.7 | c.458A>G | p.Tyr153Cys | missense_variant | 5/20 | 1 | NM_004456.5 | P4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.86e-7 AC: 1AN: 1458404Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 725456
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Weaver syndrome Other:1
not provided, no classification provided | literature only | GeneReviews | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at