rs2230562
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001961.4(EEF2):c.486C>T(p.Arg162=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000567 in 1,613,394 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.00074 ( 2 hom., cov: 33)
Exomes 𝑓: 0.00055 ( 7 hom. )
Consequence
EEF2
NM_001961.4 synonymous
NM_001961.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.05
Genes affected
EEF2 (HGNC:3214): (eukaryotic translation elongation factor 2) This gene encodes a member of the GTP-binding translation elongation factor family. This protein is an essential factor for protein synthesis. It promotes the GTP-dependent translocation of the nascent protein chain from the A-site to the P-site of the ribosome. This protein is completely inactivated by EF-2 kinase phosporylation. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 19-3982933-G-A is Benign according to our data. Variant chr19-3982933-G-A is described in ClinVar as [Benign]. Clinvar id is 585834.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-3982933-G-A is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=-4.05 with no splicing effect.
BS2
?
High AC in GnomAd4 at 112 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EEF2 | NM_001961.4 | c.486C>T | p.Arg162= | synonymous_variant | 4/15 | ENST00000309311.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EEF2 | ENST00000309311.7 | c.486C>T | p.Arg162= | synonymous_variant | 4/15 | 5 | NM_001961.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000742 AC: 113AN: 152214Hom.: 2 Cov.: 33
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GnomAD3 exomes AF: 0.00119 AC: 297AN: 249652Hom.: 5 AF XY: 0.00131 AC XY: 177AN XY: 135374
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GnomAD4 exome AF: 0.000550 AC: 803AN: 1461062Hom.: 7 Cov.: 32 AF XY: 0.000563 AC XY: 409AN XY: 726866
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GnomAD4 genome ? AF: 0.000735 AC: 112AN: 152332Hom.: 2 Cov.: 33 AF XY: 0.000832 AC XY: 62AN XY: 74482
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 01, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Feb 22, 2018 | - - |
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
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at