2-113118036-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_173841.3(IL1RN):c.10+8C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_173841.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL1RN | NM_173841.3 | c.10+8C>T | splice_region_variant, intron_variant | Intron 1 of 5 | NP_776213.1 | |||
IL1RN | NM_000577.5 | c.10+8C>T | splice_region_variant, intron_variant | Intron 1 of 4 | NP_000568.1 | |||
IL1RN | NM_001318914.2 | c.-273+8C>T | splice_region_variant, intron_variant | Intron 1 of 6 | NP_001305843.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL1RN | ENST00000259206.9 | c.10+8C>T | splice_region_variant, intron_variant | Intron 1 of 5 | 1 | ENSP00000259206.5 | ||||
IL1RN | ENST00000354115.6 | c.10+8C>T | splice_region_variant, intron_variant | Intron 1 of 4 | 1 | ENSP00000329072.3 | ||||
IL1RN | ENST00000361779.7 | c.-210+8C>T | splice_region_variant, intron_variant | Intron 1 of 5 | 1 | ENSP00000354816.3 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 29
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Sterile multifocal osteomyelitis with periostitis and pustulosis Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.