11-31509949-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6BP7
The NM_019040.5(ELP4):c.165G>T(p.Ser55Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,613,154 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 (no stars).
Frequency
Consequence
NM_019040.5 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ELP4 | NM_019040.5 | c.165G>T | p.Ser55Ser | synonymous_variant | Exon 1 of 10 | ENST00000640961.2 | NP_061913.3 | |
ELP4 | NM_001288726.2 | c.165G>T | p.Ser55Ser | synonymous_variant | Exon 1 of 12 | NP_001275655.1 | ||
ELP4 | NM_001288725.2 | c.165G>T | p.Ser55Ser | synonymous_variant | Exon 1 of 11 | NP_001275654.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000403 AC: 1AN: 247982Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134830
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461004Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726790
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74314
ClinVar
Submissions by phenotype
ELP4-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at