rs140221307
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP6BS1BS2
The NM_014339.7(IL17RA):āc.958T>Cā(p.Trp320Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00389 in 1,613,944 control chromosomes in the GnomAD database, including 19 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. W320C) has been classified as Uncertain significance.
Frequency
Consequence
NM_014339.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL17RA | NM_014339.7 | c.958T>C | p.Trp320Arg | missense_variant | 11/13 | ENST00000319363.11 | |
IL17RA | NM_001289905.2 | c.943+265T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL17RA | ENST00000319363.11 | c.958T>C | p.Trp320Arg | missense_variant | 11/13 | 1 | NM_014339.7 | P2 | |
IL17RA | ENST00000612619.2 | c.943+265T>C | intron_variant | 5 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00233 AC: 355AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00173 AC: 435AN: 251206Hom.: 0 AF XY: 0.00170 AC XY: 231AN XY: 135808
GnomAD4 exome AF: 0.00405 AC: 5917AN: 1461626Hom.: 19 Cov.: 33 AF XY: 0.00386 AC XY: 2806AN XY: 727132
GnomAD4 genome AF: 0.00233 AC: 355AN: 152318Hom.: 0 Cov.: 33 AF XY: 0.00223 AC XY: 166AN XY: 74480
ClinVar
Submissions by phenotype
Immunodeficiency 51 Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago | Mar 30, 2021 | IL17RA NM_014339.6 exon 11 p.Trp320Arg (c.958T>C): This variant has been reported in the literature in 1 individual with sarcoidosis, segregating with disease in 2 affected family members; of note, additional variants were identified in this family that the authors believed were suggestive of disease (Besnard 2018 PMID:29554915). This variant is present in 0.3% (443/129026) of European alleles in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/22-17586757-T-C?dataset=gnomad_r2_1). This variant is present in ClinVar (Variation ID:340587). Evolutionary conservation and computational predictive tools suggest that this variant may impact the protein. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain. - |
Familial Candidiasis, Recessive Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at