chr7-148832759-G-GA
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_004456.5(EZH2):c.247-10dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00407 in 1,555,412 control chromosomes in the GnomAD database, including 19 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_004456.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EZH2 | NM_004456.5 | c.247-10dupT | intron_variant | Intron 3 of 19 | ENST00000320356.7 | NP_004447.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00295 AC: 448AN: 151854Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00286 AC: 691AN: 241264Hom.: 1 AF XY: 0.00287 AC XY: 376AN XY: 130924
GnomAD4 exome AF: 0.00419 AC: 5887AN: 1403440Hom.: 19 Cov.: 22 AF XY: 0.00406 AC XY: 2843AN XY: 700048
GnomAD4 genome AF: 0.00295 AC: 448AN: 151972Hom.: 0 Cov.: 32 AF XY: 0.00269 AC XY: 200AN XY: 74286
ClinVar
Submissions by phenotype
Weaver syndrome Benign:2
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EZH2-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
See Variant Classification Assertion Criteria. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at