rs145221454
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PP5BP4BS2_Supporting
The NM_017563.5(IL17RD):c.1403C>T(p.Ser468Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000403 in 1,613,868 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 Pathogenic (no stars).
Frequency
Consequence
NM_017563.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL17RD | NM_017563.5 | c.1403C>T | p.Ser468Leu | missense_variant | 12/13 | ENST00000296318.12 | NP_060033.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL17RD | ENST00000296318.12 | c.1403C>T | p.Ser468Leu | missense_variant | 12/13 | 1 | NM_017563.5 | ENSP00000296318 | P1 | |
IL17RD | ENST00000320057.9 | c.971C>T | p.Ser324Leu | missense_variant | 13/14 | 1 | ENSP00000322250 | |||
IL17RD | ENST00000463523.5 | c.971C>T | p.Ser324Leu | missense_variant | 12/13 | 1 | ENSP00000417516 | |||
IL17RD | ENST00000469841.5 | n.1340C>T | non_coding_transcript_exon_variant | 12/12 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251136Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135734
GnomAD4 exome AF: 0.0000410 AC: 60AN: 1461692Hom.: 0 Cov.: 34 AF XY: 0.0000385 AC XY: 28AN XY: 727134
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74354
ClinVar
Submissions by phenotype
Hypogonadotropic hypogonadism 18 with anosmia Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | May 02, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at