2-102019740-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_004633.4(IL1R2):c.616C>T(p.Arg206Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000248 in 1,613,990 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_004633.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL1R2 | ENST00000332549.8 | c.616C>T | p.Arg206Cys | missense_variant | Exon 5 of 9 | 1 | NM_004633.4 | ENSP00000330959.3 | ||
IL1R2 | ENST00000393414.6 | c.616C>T | p.Arg206Cys | missense_variant | Exon 5 of 9 | 1 | ENSP00000377066.2 | |||
IL1R2 | ENST00000441002.1 | c.616C>T | p.Arg206Cys | missense_variant | Exon 4 of 6 | 1 | ENSP00000414611.1 | |||
IL1R2 | ENST00000457817.5 | c.616C>T | p.Arg206Cys | missense_variant | Exon 5 of 5 | 2 | ENSP00000408415.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152226Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251308Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135844
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1461764Hom.: 0 Cov.: 31 AF XY: 0.0000316 AC XY: 23AN XY: 727194
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152226Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.616C>T (p.R206C) alteration is located in exon 5 (coding exon 4) of the IL1R2 gene. This alteration results from a C to T substitution at nucleotide position 616, causing the arginine (R) at amino acid position 206 to be replaced by a cysteine (C). 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