rs878972
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000259206.9(IL1RN):c.73+8A>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 1,604,640 control chromosomes in the GnomAD database, including 56,618 homozygotes. 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 Benign (★★).
Frequency
Consequence
ENST00000259206.9 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL1RN | NM_000577.5 | c.10+2108A>C | intron_variant | ||||
IL1RN | NM_001318914.2 | c.-210+8A>C | splice_region_variant, intron_variant | ||||
IL1RN | NM_173841.3 | c.73+8A>C | splice_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL1RN | ENST00000259206.9 | c.73+8A>C | splice_region_variant, intron_variant | 1 | |||||
IL1RN | ENST00000354115.6 | c.10+2108A>C | intron_variant | 1 | A1 | ||||
IL1RN | ENST00000361779.7 | c.-209-1312A>C | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.210 AC: 31746AN: 151264Hom.: 4064 Cov.: 30
GnomAD3 exomes AF: 0.253 AC: 63662AN: 251238Hom.: 9001 AF XY: 0.256 AC XY: 34830AN XY: 135800
GnomAD4 exome AF: 0.263 AC: 382285AN: 1453256Hom.: 52548 Cov.: 29 AF XY: 0.263 AC XY: 190375AN XY: 723634
GnomAD4 genome ? AF: 0.210 AC: 31763AN: 151384Hom.: 4070 Cov.: 30 AF XY: 0.212 AC XY: 15694AN XY: 73864
ClinVar
Submissions by phenotype
not specified Benign:4
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Nov 12, 2023 | This variant is classified as Benign based on local population frequency. This variant was detected in 49% of patients studied by a panel of primary immunodeficiencies. Number of patients: 47. Only high quality variants are reported. - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Sterile multifocal osteomyelitis with periostitis and pustulosis Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 12, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at