chr19-3976624-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_001961.4(EEF2):c.2507C>T(p.Ala836Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000186 in 1,610,312 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. A836A) has been classified as Likely benign.
Frequency
Consequence
NM_001961.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EEF2 | NM_001961.4 | c.2507C>T | p.Ala836Val | missense_variant | 15/15 | ENST00000309311.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EEF2 | ENST00000309311.7 | c.2507C>T | p.Ala836Val | missense_variant | 15/15 | 5 | NM_001961.4 | P1 | |
EEF2 | ENST00000600794.1 | c.108-324C>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000458 AC: 11AN: 240294Hom.: 0 AF XY: 0.0000689 AC XY: 9AN XY: 130718
GnomAD4 exome AF: 0.0000199 AC: 29AN: 1457988Hom.: 0 Cov.: 31 AF XY: 0.0000221 AC XY: 16AN XY: 725002
GnomAD4 genome ? AF: 0.00000656 AC: 1AN: 152324Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74486
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Dec 06, 2022 | Available data are insufficient to determine the clinical significance of the variant at this time. The frequency of this variant in the general population is higher than would generally be expected for pathogenic variants in this gene (http://gnomad.broadinstitute.org). Computational tools predict that this variant is not damaging. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at