22-17102216-G-C
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The ENST00000319363.11(IL17RA):āc.676G>Cā(p.Glu226Gln) variant causes a missense change. The variant allele was found at a frequency of 0.000246 in 1,614,052 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 Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E226K) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000319363.11 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL17RA | NM_014339.7 | c.676G>C | p.Glu226Gln | missense_variant | 7/13 | ENST00000319363.11 | NP_055154.3 | |
IL17RA | NM_001289905.2 | c.676G>C | p.Glu226Gln | missense_variant | 7/12 | NP_001276834.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL17RA | ENST00000319363.11 | c.676G>C | p.Glu226Gln | missense_variant | 7/13 | 1 | NM_014339.7 | ENSP00000320936 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000493 AC: 75AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000382 AC: 96AN: 251488Hom.: 0 AF XY: 0.000338 AC XY: 46AN XY: 135918
GnomAD4 exome AF: 0.000220 AC: 322AN: 1461880Hom.: 1 Cov.: 33 AF XY: 0.000215 AC XY: 156AN XY: 727242
GnomAD4 genome AF: 0.000493 AC: 75AN: 152172Hom.: 0 Cov.: 32 AF XY: 0.000673 AC XY: 50AN XY: 74344
ClinVar
Submissions by phenotype
Immunodeficiency 51 Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 12, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at