20-63493195-G-C
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001958.5(EEF1A2):āc.714C>Gā(p.Pro238=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000284 in 1,548,664 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 (ā ā ). Synonymous variant affecting the same amino acid position (i.e. P238P) 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 -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EEF1A2 | NM_001958.5 | c.714C>G | p.Pro238= | synonymous_variant | 5/8 | ENST00000217182.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EEF1A2 | ENST00000217182.6 | c.714C>G | p.Pro238= | synonymous_variant | 5/8 | 1 | NM_001958.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152078Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000977 AC: 15AN: 153540Hom.: 0 AF XY: 0.0000740 AC XY: 6AN XY: 81032
GnomAD4 exome AF: 0.0000236 AC: 33AN: 1396468Hom.: 0 Cov.: 32 AF XY: 0.0000174 AC XY: 12AN XY: 688668
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152196Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74396
ClinVar
Submissions by phenotype
Developmental and epileptic encephalopathy, 33 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 05, 2024 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 14, 2017 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at