chr19-3976671-C-G
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_001961.4(EEF2):c.2460G>C(p.Leu820=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00163 in 1,608,438 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. L820L) has been classified as Likely benign.
Frequency
Consequence
NM_001961.4 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EEF2 | NM_001961.4 | c.2460G>C | p.Leu820= | synonymous_variant | 15/15 | ENST00000309311.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EEF2 | ENST00000309311.7 | c.2460G>C | p.Leu820= | synonymous_variant | 15/15 | 5 | NM_001961.4 | P1 | |
EEF2 | ENST00000600794.1 | c.108-371G>C | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00142 AC: 216AN: 152214Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00150 AC: 357AN: 237632Hom.: 0 AF XY: 0.00152 AC XY: 196AN XY: 129304
GnomAD4 exome AF: 0.00165 AC: 2401AN: 1456106Hom.: 4 Cov.: 31 AF XY: 0.00164 AC XY: 1190AN XY: 724092
GnomAD4 genome ? AF: 0.00142 AC: 216AN: 152332Hom.: 0 Cov.: 33 AF XY: 0.00136 AC XY: 101AN XY: 74492
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 26, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 21, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jun 10, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at