chr22-17085110-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS1
The NM_014339.7(IL17RA):c.19C>T(p.Pro7Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000358 in 1,373,346 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P7L) has been classified as Likely benign.
Frequency
Consequence
NM_014339.7 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL17RA | NM_014339.7 | c.19C>T | p.Pro7Ser | missense_variant | 1/13 | ENST00000319363.11 | |
IL17RA | NM_001289905.2 | c.19C>T | p.Pro7Ser | missense_variant | 1/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL17RA | ENST00000319363.11 | c.19C>T | p.Pro7Ser | missense_variant | 1/13 | 1 | NM_014339.7 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00183 AC: 279AN: 152154Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000150 AC: 4AN: 26720Hom.: 0 AF XY: 0.000122 AC XY: 2AN XY: 16396
GnomAD4 exome AF: 0.000173 AC: 211AN: 1221082Hom.: 1 Cov.: 60 AF XY: 0.000158 AC XY: 94AN XY: 593700
GnomAD4 genome ? AF: 0.00184 AC: 280AN: 152264Hom.: 1 Cov.: 33 AF XY: 0.00184 AC XY: 137AN XY: 74446
ClinVar
Submissions by phenotype
Immunodeficiency 51 Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jul 25, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 08, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at