rs1420096
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003855.5(IL18R1):c.1112-17C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 1,570,424 control chromosomes in the GnomAD database, including 185,344 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_003855.5 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL18R1 | NM_003855.5 | c.1112-17C>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000233957.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL18R1 | ENST00000233957.7 | c.1112-17C>T | splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_003855.5 | P1 | |||
IL18R1 | ENST00000409599.5 | c.1112-17C>T | splice_polypyrimidine_tract_variant, intron_variant | 5 | P1 | ||||
IL18R1 | ENST00000410040.5 | c.1112-17C>T | splice_polypyrimidine_tract_variant, intron_variant | 2 | |||||
IL18R1 | ENST00000677287.1 | c.*656-17C>T | splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.535 AC: 81178AN: 151832Hom.: 23543 Cov.: 31
GnomAD3 exomes AF: 0.434 AC: 102512AN: 236108Hom.: 25395 AF XY: 0.428 AC XY: 54775AN XY: 127916
GnomAD4 exome AF: 0.466 AC: 661291AN: 1418474Hom.: 161770 Cov.: 25 AF XY: 0.460 AC XY: 324579AN XY: 705122
GnomAD4 genome ? AF: 0.535 AC: 81262AN: 151950Hom.: 23574 Cov.: 31 AF XY: 0.529 AC XY: 39240AN XY: 74232
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at