chr6-52236954-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PP3_Moderate
The NM_052872.4(IL17F):c.469C>T(p.Pro157Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000057 in 1,613,876 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 Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P157A) has been classified as Uncertain significance.
Frequency
Consequence
NM_052872.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL17F | NM_052872.4 | c.469C>T | p.Pro157Ser | missense_variant | 3/3 | ENST00000336123.5 | |
IL17F | XM_011514276.1 | c.469C>T | p.Pro157Ser | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL17F | ENST00000336123.5 | c.469C>T | p.Pro157Ser | missense_variant | 3/3 | 1 | NM_052872.4 | P1 | |
IL17F | ENST00000478427.1 | n.653C>T | non_coding_transcript_exon_variant | 2/2 | 1 | ||||
IL17F | ENST00000699946.1 | c.469C>T | p.Pro157Ser | missense_variant | 4/4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152206Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 251008Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135654
GnomAD4 exome AF: 0.0000602 AC: 88AN: 1461552Hom.: 0 Cov.: 30 AF XY: 0.0000633 AC XY: 46AN XY: 727100
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152324Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74482
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 10, 2022 | The c.469C>T (p.P157S) alteration is located in exon 3 (coding exon 3) of the IL17F gene. This alteration results from a C to T substitution at nucleotide position 469, causing the proline (P) at amino acid position 157 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Candidiasis, familial, 6 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at