chr11-86245273-T-G
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_003797.5(EED):c.44T>G(p.Met15Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00000744 in 1,613,348 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M15V) 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 -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EED | NM_003797.5 | c.44T>G | p.Met15Arg | missense_variant | 1/12 | ENST00000263360.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EED | ENST00000263360.11 | c.44T>G | p.Met15Arg | missense_variant | 1/12 | 1 | NM_003797.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151974Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.00000813 AC: 2AN: 245958Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 133584
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461374Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 726958
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151974Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 74218
ClinVar
Submissions by phenotype
Cohen-Gibson syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Oct 29, 2021 | 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. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. This variant has not been reported in the literature in individuals affected with EED-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.003%). This sequence change replaces methionine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 15 of the EED protein (p.Met15Arg). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at