chr22-50000854-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001371417.1(IL17REL):c.290G>A(p.Arg97Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000185 in 1,565,112 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_001371417.1 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 |
---|---|---|---|---|---|---|---|
IL17REL | NM_001371417.1 | c.290G>A | p.Arg97Gln | missense_variant | 4/15 | ENST00000695950.1 | |
IL17REL | NM_001371416.1 | c.290G>A | p.Arg97Gln | missense_variant | 4/15 | ||
IL17REL | NM_001001694.3 | c.119G>A | p.Arg40Gln | missense_variant | 5/15 | ||
IL17REL | XR_001755245.2 | n.409G>A | non_coding_transcript_exon_variant | 4/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL17REL | ENST00000695950.1 | c.290G>A | p.Arg97Gln | missense_variant | 4/15 | NM_001371417.1 | A2 | ||
IL17REL | ENST00000695951.1 | c.290G>A | p.Arg97Gln | missense_variant | 4/15 | P2 | |||
IL17REL | ENST00000389983.7 | c.*254G>A | 3_prime_UTR_variant, NMD_transcript_variant | 5/15 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152208Hom.: 0 Cov.: 34
GnomAD4 exome AF: 0.0000184 AC: 26AN: 1412904Hom.: 0 Cov.: 33 AF XY: 0.0000186 AC XY: 13AN XY: 700048
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152208Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 25, 2022 | The c.119G>A (p.R40Q) alteration is located in exon 5 (coding exon 2) of the IL17REL gene. This alteration results from a G to A substitution at nucleotide position 119, causing the arginine (R) at amino acid position 40 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at