chr11-72000347-T-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001039660.2(IL18BP):c.29-4T>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000502 in 1,613,420 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001039660.2 splice_region, splice_polypyrimidine_tract, intron
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL18BP | NM_001039660.2 | c.29-4T>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000393703.9 | NP_001034749.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL18BP | ENST00000393703.9 | c.29-4T>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 3 | NM_001039660.2 | ENSP00000377306 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000363 AC: 9AN: 248110Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134758
GnomAD4 exome AF: 0.0000506 AC: 74AN: 1461118Hom.: 0 Cov.: 32 AF XY: 0.0000413 AC XY: 30AN XY: 726924
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152302Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74462
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 05, 2023 | This sequence change falls in intron 1 of the IL18BP gene. It does not directly change the encoded amino acid sequence of the IL18BP protein. This variant is present in population databases (rs755777463, gnomAD 0.005%). This variant has not been reported in the literature in individuals affected with IL18BP-related conditions. ClinVar contains an entry for this variant (Variation ID: 1985233). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at