rs755919625
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_153460.4(IL17RC):c.2152G>A(p.Asp718Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000326 in 1,596,632 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★★).
Frequency
Consequence
NM_153460.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL17RC | NM_153460.4 | c.2152G>A | p.Asp718Asn | missense_variant | 19/19 | ENST00000403601.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL17RC | ENST00000403601.8 | c.2152G>A | p.Asp718Asn | missense_variant | 19/19 | 1 | NM_153460.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152202Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000153 AC: 34AN: 221706Hom.: 0 AF XY: 0.000138 AC XY: 17AN XY: 123032
GnomAD4 exome AF: 0.0000284 AC: 41AN: 1444430Hom.: 0 Cov.: 33 AF XY: 0.0000279 AC XY: 20AN XY: 717706
GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152202Hom.: 0 Cov.: 34 AF XY: 0.0000941 AC XY: 7AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 15, 2022 | The c.2365G>A (p.D789N) alteration is located in exon 19 (coding exon 19) of the IL17RC gene. This alteration results from a G to A substitution at nucleotide position 2365, causing the aspartic acid (D) at amino acid position 789 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Candidiasis, familial, 9 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Dec 11, 2023 | This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 789 of the IL17RC protein (p.Asp789Asn). This variant is present in population databases (rs755919625, gnomAD 0.09%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with IL17RC-related conditions. ClinVar contains an entry for this variant (Variation ID: 567761). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at