chr11-86245245-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_003797.5(EED):c.16G>A(p.Val6Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000273 in 1,613,342 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V6A) has been classified as Uncertain significance.
Frequency
Consequence
NM_003797.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EED | NM_003797.5 | c.16G>A | p.Val6Met | missense_variant | 1/12 | ENST00000263360.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EED | ENST00000263360.11 | c.16G>A | p.Val6Met | missense_variant | 1/12 | 1 | NM_003797.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 151998Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000202 AC: 5AN: 247180Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134170
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1461344Hom.: 0 Cov.: 31 AF XY: 0.0000289 AC XY: 21AN XY: 726948
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 151998Hom.: 0 Cov.: 30 AF XY: 0.0000269 AC XY: 2AN XY: 74220
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 29, 2021 | The c.16G>A (p.V6M) alteration is located in exon 1 (coding exon 1) of the EED gene. This alteration results from a G to A substitution at nucleotide position 16, causing the valine (V) at amino acid position 6 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at