2-102192082-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_003854.4(IL1RL2):c.451C>T(p.Pro151Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000113 in 1,599,756 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003854.4 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 |
---|---|---|---|---|---|---|---|---|---|---|
IL1RL2 | ENST00000264257.7 | c.451C>T | p.Pro151Ser | missense_variant | Exon 4 of 12 | 1 | NM_003854.4 | ENSP00000264257.2 | ||
IL1RL2 | ENST00000441515.3 | c.138+4157C>T | intron_variant | Intron 2 of 9 | 1 | ENSP00000413348.2 | ||||
IL1RL2 | ENST00000421464.1 | c.451C>T | p.Pro151Ser | missense_variant | Exon 4 of 5 | 5 | ENSP00000387611.1 | |||
IL1RL2 | ENST00000481806.1 | n.151+4157C>T | intron_variant | Intron 2 of 9 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152106Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000430 AC: 1AN: 232478Hom.: 0 AF XY: 0.00000794 AC XY: 1AN XY: 126014
GnomAD4 exome AF: 0.00000622 AC: 9AN: 1447650Hom.: 0 Cov.: 30 AF XY: 0.00000695 AC XY: 5AN XY: 719744
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152106Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74292
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.451C>T (p.P151S) alteration is located in exon 4 (coding exon 3) of the IL1RL2 gene. This alteration results from a C to T substitution at nucleotide position 451, causing the proline (P) at amino acid position 151 to be replaced by a serine (S). 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