NM_003797.5:c.36A>G
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_003797.5(EED):c.36A>G(p.Gly12Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 30)
Consequence
EED
NM_003797.5 synonymous
NM_003797.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.84
Publications
1 publications found
Genes affected
EED (HGNC:3188): (embryonic ectoderm development) This gene encodes a member of the Polycomb-group (PcG) family. PcG family members form multimeric protein complexes, which are involved in maintaining the transcriptional repressive state of genes over successive cell generations. This protein interacts with enhancer of zeste 2, the cytoplasmic tail of integrin beta7, immunodeficiency virus type 1 (HIV-1) MA protein, and histone deacetylase proteins. This protein mediates repression of gene activity through histone deacetylation, and may act as a specific regulator of integrin function. Two transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
EED Gene-Disease associations (from GenCC):
- Cohen-Gibson syndromeInheritance: AD Classification: STRONG, MODERATE Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae), ClinGen
- Weaver syndromeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (REVEL=0.032).
BP6
Variant 11-86245265-A-G is Benign according to our data. Variant chr11-86245265-A-G is described in ClinVar as Likely_benign. ClinVar VariationId is 1987507.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.84 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_003797.5. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| EED | TSL:1 MANE Select | c.36A>G | p.Gly12Gly | synonymous | Exon 1 of 12 | ENSP00000263360.6 | O75530-1 | ||
| EED | TSL:1 | c.36A>G | p.Gly12Gly | synonymous | Exon 1 of 13 | ENSP00000338186.5 | O75530-2 | ||
| EED | TSL:1 | c.36A>G | p.Gly12Gly | synonymous | Exon 1 of 11 | ENSP00000315587.4 | O75530-3 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
30
GnomAD2 exomes AF: 0.00000407 AC: 1AN: 245606 AF XY: 0.00 show subpopulations
GnomAD2 exomes
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AC:
1
AN:
245606
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GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome
GnomAD4 genome
Cov.:
30
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ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
Cohen-Gibson syndrome (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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