chr11-86245307-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_003797.5(EED):c.78C>T(p.Asp26=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,613,248 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 Likely benign (★).
Frequency
Genomes: 𝑓 0.000079 ( 0 hom., cov: 30)
Exomes 𝑓: 0.000012 ( 0 hom. )
Consequence
EED
NM_003797.5 synonymous
NM_003797.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.648
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.35).
BP6
?
Variant 11-86245307-C-T is Benign according to our data. Variant chr11-86245307-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1130122.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.648 with no splicing effect.
BS2
?
High AC in GnomAd at 12 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EED | NM_003797.5 | c.78C>T | p.Asp26= | synonymous_variant | 1/12 | ENST00000263360.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EED | ENST00000263360.11 | c.78C>T | p.Asp26= | synonymous_variant | 1/12 | 1 | NM_003797.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000790 AC: 12AN: 151934Hom.: 0 Cov.: 30
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GnomAD3 exomes AF: 0.0000286 AC: 7AN: 244908Hom.: 0 AF XY: 0.0000301 AC XY: 4AN XY: 133060
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GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461314Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 726920
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GnomAD4 genome ? AF: 0.0000790 AC: 12AN: 151934Hom.: 0 Cov.: 30 AF XY: 0.0000943 AC XY: 7AN XY: 74192
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Cohen-Gibson syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at