chr11-31509877-G-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_019040.5(ELP4):c.93G>T(p.Arg31Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,614,068 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign 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 Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ELP4 | NM_019040.5 | c.93G>T | p.Arg31Ser | missense_variant | Exon 1 of 10 | ENST00000640961.2 | NP_061913.3 | |
ELP4 | NM_001288726.2 | c.93G>T | p.Arg31Ser | missense_variant | Exon 1 of 12 | NP_001275655.1 | ||
ELP4 | NM_001288725.2 | c.93G>T | p.Arg31Ser | missense_variant | Exon 1 of 11 | NP_001275654.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152228Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249428Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135344
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461840Hom.: 1 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727212
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74374
ClinVar
Submissions by phenotype
not provided Uncertain:1
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. 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. This variant has not been reported in the literature in individuals affected with ELP4-related conditions. This variant is present in population databases (rs373816333, gnomAD 0.009%). This sequence change replaces arginine, which is basic and polar, with serine, which is neutral and polar, at codon 31 of the ELP4 protein (p.Arg31Ser). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at