chr20-63494979-G-A
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001958.5(EEF1A2):c.447C>T(p.Ile149=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000151 in 1,460,460 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. I149I) 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 -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EEF1A2 | NM_001958.5 | c.447C>T | p.Ile149= | synonymous_variant | 4/8 | ENST00000217182.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EEF1A2 | ENST00000217182.6 | c.447C>T | p.Ile149= | synonymous_variant | 4/8 | 1 | NM_001958.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 250202Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135752
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1460460Hom.: 0 Cov.: 35 AF XY: 0.0000179 AC XY: 13AN XY: 726522
GnomAD4 genome Cov.: 34
ClinVar
Submissions by phenotype
Developmental and epileptic encephalopathy, 33 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 27, 2023 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 24, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at