chr2-102225961-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003854.4(IL1RL2):c.1055T>C(p.Val352Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000891 in 1,459,412 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign 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. V352I) has been classified as Benign.
Frequency
Consequence
NM_003854.4 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 |
---|---|---|---|---|---|---|---|
IL1RL2 | NM_003854.4 | c.1055T>C | p.Val352Ala | missense_variant | 9/12 | ENST00000264257.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL1RL2 | ENST00000264257.7 | c.1055T>C | p.Val352Ala | missense_variant | 9/12 | 1 | NM_003854.4 | P1 | |
IL1RL2 | ENST00000441515.3 | c.701T>C | p.Val234Ala | missense_variant | 7/10 | 1 | |||
IL1RL2 | ENST00000481806.1 | n.717T>C | non_coding_transcript_exon_variant | 7/10 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000801 AC: 2AN: 249720Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135110
GnomAD4 exome AF: 0.00000891 AC: 13AN: 1459412Hom.: 0 Cov.: 30 AF XY: 0.00000826 AC XY: 6AN XY: 726064
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 18, 2023 | The c.1055T>C (p.V352A) alteration is located in exon 9 (coding exon 8) of the IL1RL2 gene. This alteration results from a T to C substitution at nucleotide position 1055, causing the valine (V) at amino acid position 352 to be replaced by an alanine (A). 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