11-31520069-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_019040.5(ELP4):c.237C>T(p.Ala79Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,612,430 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
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ELP4 | NM_019040.5 | c.237C>T | p.Ala79Ala | synonymous_variant | Exon 2 of 10 | ENST00000640961.2 | NP_061913.3 | |
ELP4 | NM_001288726.2 | c.237C>T | p.Ala79Ala | synonymous_variant | Exon 2 of 12 | NP_001275655.1 | ||
ELP4 | NM_001288725.2 | c.237C>T | p.Ala79Ala | synonymous_variant | Exon 2 of 11 | NP_001275654.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152076Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 248490Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134840
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1460354Hom.: 0 Cov.: 29 AF XY: 0.0000151 AC XY: 11AN XY: 726526
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152076Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74280
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