11-86245272-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_003797.5(EED):c.43A>G(p.Met15Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000384 in 1,613,582 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. M15R) has been classified as Uncertain significance.
Frequency
Consequence
NM_003797.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
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.43A>G | p.Met15Val | missense_variant | 1/12 | ENST00000263360.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EED | ENST00000263360.11 | c.43A>G | p.Met15Val | missense_variant | 1/12 | 1 | NM_003797.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152064Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000284 AC: 7AN: 246118Hom.: 0 AF XY: 0.00000748 AC XY: 1AN XY: 133668
GnomAD4 exome AF: 0.0000397 AC: 58AN: 1461404Hom.: 0 Cov.: 31 AF XY: 0.0000399 AC XY: 29AN XY: 726978
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152178Hom.: 0 Cov.: 30 AF XY: 0.0000134 AC XY: 1AN XY: 74394
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 04, 2023 | The c.43A>G (p.M15V) alteration is located in exon 1 (coding exon 1) of the EED gene. This alteration results from a A to G substitution at nucleotide position 43, causing the methionine (M) at amino acid position 15 to be replaced by a valine (V). 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