chr3-9918386-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_153460.4(IL17RC):c.332C>T(p.Ser111Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 1,607,902 control chromosomes in the GnomAD database, including 215,790 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_153460.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL17RC | NM_153460.4 | c.332C>T | p.Ser111Leu | missense_variant | 4/19 | ENST00000403601.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL17RC | ENST00000403601.8 | c.332C>T | p.Ser111Leu | missense_variant | 4/19 | 1 | NM_153460.4 | P4 |
Frequencies
GnomAD3 genomes AF: 0.502 AC: 76339AN: 151956Hom.: 19821 Cov.: 32
GnomAD3 exomes AF: 0.463 AC: 111494AN: 240610Hom.: 27822 AF XY: 0.464 AC XY: 60319AN XY: 130092
GnomAD4 exome AF: 0.511 AC: 743368AN: 1455828Hom.: 195934 Cov.: 42 AF XY: 0.507 AC XY: 367126AN XY: 723878
GnomAD4 genome AF: 0.503 AC: 76420AN: 152074Hom.: 19856 Cov.: 32 AF XY: 0.499 AC XY: 37090AN XY: 74326
ClinVar
Submissions by phenotype
Candidiasis, familial, 9 Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 19, 2021 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jan 24, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 68% of patients studied by a panel of primary immunodeficiencies. Number of patients: 65. Only high quality variants are reported. - |
not provided Other:1
not provided, no classification provided | phenotyping only | GenomeConnect, ClinGen | - | Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at