20-63488307-C-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_001958.5(EEF1A2):c.1383G>T(p.Ala461Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000288 in 1,389,334 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 (★). Synonymous variant affecting the same amino acid position (i.e. A461A) has been classified as Likely benign.
Frequency
Consequence
NM_001958.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000664 AC: 1AN: 150708Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000101 AC: 8AN: 78940Hom.: 0 AF XY: 0.000177 AC XY: 8AN XY: 45134
GnomAD4 exome AF: 0.0000315 AC: 39AN: 1238626Hom.: 0 Cov.: 33 AF XY: 0.0000476 AC XY: 29AN XY: 609232
GnomAD4 genome AF: 0.00000664 AC: 1AN: 150708Hom.: 0 Cov.: 33 AF XY: 0.0000136 AC XY: 1AN XY: 73544
ClinVar
Submissions by phenotype
Developmental and epileptic encephalopathy, 33 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at