rs1057519079
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP3_StrongPP5
The NM_014339.7(IL17RA):c.1159G>A(p.Asp387Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000041 in 1,461,652 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 Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. D387D) has been classified as Likely benign.
Frequency
Consequence
NM_014339.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL17RA | NM_014339.7 | c.1159G>A | p.Asp387Asn | missense_variant | 13/13 | ENST00000319363.11 | |
IL17RA | NM_001289905.2 | c.1057G>A | p.Asp353Asn | missense_variant | 12/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL17RA | ENST00000319363.11 | c.1159G>A | p.Asp387Asn | missense_variant | 13/13 | 1 | NM_014339.7 | P2 | |
IL17RA | ENST00000612619.2 | c.1057G>A | p.Asp353Asn | missense_variant | 12/12 | 5 | A2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461652Hom.: 0 Cov.: 56 AF XY: 0.00000275 AC XY: 2AN XY: 727100
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Immunodeficiency 51 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Dec 19, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at