19-3977978-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_001961.4(EEF2):c.1908C>T(p.Ala636=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000219 in 1,613,038 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. A636A) has been classified as Likely benign.
Frequency
Consequence
NM_001961.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EEF2 | NM_001961.4 | c.1908C>T | p.Ala636= | synonymous_variant | 12/15 | ENST00000309311.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EEF2 | ENST00000309311.7 | c.1908C>T | p.Ala636= | synonymous_variant | 12/15 | 5 | NM_001961.4 | P1 | |
EEF2 | ENST00000600794.1 | c.107+50C>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000128 AC: 32AN: 249890Hom.: 0 AF XY: 0.000126 AC XY: 17AN XY: 135426
GnomAD4 exome AF: 0.000231 AC: 337AN: 1460784Hom.: 1 Cov.: 32 AF XY: 0.000202 AC XY: 147AN XY: 726666
GnomAD4 genome AF: 0.000112 AC: 17AN: 152254Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74448
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 12, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at