11-31520077-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PP3_ModerateBS2
The NM_019040.5(ELP4):āc.245C>Gā(p.Thr82Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000583 in 1,612,602 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 (ā ).
Frequency
Consequence
NM_019040.5 missense
Scores
Clinical Significance
Conservation
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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.245C>G | p.Thr82Arg | missense_variant | Exon 2 of 10 | ENST00000640961.2 | NP_061913.3 | |
ELP4 | NM_001288726.2 | c.245C>G | p.Thr82Arg | missense_variant | Exon 2 of 12 | NP_001275655.1 | ||
ELP4 | NM_001288725.2 | c.245C>G | p.Thr82Arg | missense_variant | Exon 2 of 11 | NP_001275654.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000242 AC: 6AN: 248424Hom.: 0 AF XY: 0.0000445 AC XY: 6AN XY: 134818
GnomAD4 exome AF: 0.0000596 AC: 87AN: 1460334Hom.: 0 Cov.: 29 AF XY: 0.0000592 AC XY: 43AN XY: 726538
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152268Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74460
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.245C>G (p.T82R) alteration is located in exon 2 (coding exon 2) of the ELP4 gene. This alteration results from a C to G substitution at nucleotide position 245, causing the threonine (T) at amino acid position 82 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at