11-31594876-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PP3_StrongBS2
The NM_019040.5(ELP4):c.488G>A(p.Arg163His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000429 in 1,560,200 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_019040.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ELP4 | NM_019040.5 | c.488G>A | p.Arg163His | missense_variant | Exon 4 of 10 | ENST00000640961.2 | NP_061913.3 | |
ELP4 | NM_001288726.2 | c.488G>A | p.Arg163His | missense_variant | Exon 4 of 12 | NP_001275655.1 | ||
ELP4 | NM_001288725.2 | c.488G>A | p.Arg163His | missense_variant | Exon 4 of 11 | NP_001275654.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152032Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000246 AC: 5AN: 202904Hom.: 0 AF XY: 0.0000269 AC XY: 3AN XY: 111424
GnomAD4 exome AF: 0.0000348 AC: 49AN: 1408050Hom.: 0 Cov.: 29 AF XY: 0.0000358 AC XY: 25AN XY: 698874
GnomAD4 genome AF: 0.000118 AC: 18AN: 152150Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74380
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.488G>A (p.R163H) alteration is located in exon 4 (coding exon 4) of the ELP4 gene. This alteration results from a G to A substitution at nucleotide position 488, causing the arginine (R) at amino acid position 163 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
not provided Uncertain:1
An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. ClinVar contains an entry for this variant (Variation ID: 2517420). This variant has not been reported in the literature in individuals affected with ELP4-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 163 of the ELP4 protein (p.Arg163His). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at