19-3978116-G-C
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_001961.4(EEF2):c.1770C>G(p.Leu590=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000133 in 1,507,842 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. L590L) has been classified as Benign.
Frequency
Consequence
NM_001961.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EEF2 | NM_001961.4 | c.1770C>G | p.Leu590= | synonymous_variant | 12/15 | ENST00000309311.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EEF2 | ENST00000309311.7 | c.1770C>G | p.Leu590= | synonymous_variant | 12/15 | 5 | NM_001961.4 | P1 | |
EEF2 | ENST00000600794.1 | c.21C>G | p.Leu7= | synonymous_variant | 1/2 | 3 | |||
EEF2 | ENST00000596417.1 | n.188C>G | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152156Hom.: 0 Cov.: 32
GnomAD4 exome AF: 7.38e-7 AC: 1AN: 1355686Hom.: 0 Cov.: 32 AF XY: 0.00000151 AC XY: 1AN XY: 661316
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152156Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74312
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at