rs111392970
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001958.5(EEF1A2):c.1029+3G>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000151 in 1,606,092 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001958.5 splice_region, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152174Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000121 AC: 30AN: 246996Hom.: 0 AF XY: 0.000104 AC XY: 14AN XY: 134446
GnomAD4 exome AF: 0.000162 AC: 236AN: 1453798Hom.: 0 Cov.: 33 AF XY: 0.000169 AC XY: 122AN XY: 721730
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152294Hom.: 0 Cov.: 34 AF XY: 0.0000537 AC XY: 4AN XY: 74464
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Jan 13, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2022 | EEF1A2: BP4 - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 01, 2020 | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 23, 2018 | The c.1029+3G>T intronic variant results from a G to T substitution 3 nucleotides after coding exon 5 in the EEF1A2 gene. This variant did not co-segregate with disease in one individual tested in our laboratory. This nucleotide position is poorly conserved in available vertebrate species. Using the BDGP and ESEfinder splice site prediction tools, this alteration is predicted to weaken the efficiency of the native splice donor site; however, direct evidence is unavailable. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Developmental and epileptic encephalopathy, 33 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 17, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at