rs419598
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_173842.3(IL1RN):c.171T>C(p.Ala57Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 1,609,674 control chromosomes in the GnomAD database, including 59,383 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_173842.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.216 AC: 32829AN: 152038Hom.: 4280 Cov.: 32
GnomAD3 exomes AF: 0.256 AC: 64470AN: 251432Hom.: 9252 AF XY: 0.259 AC XY: 35246AN XY: 135884
GnomAD4 exome AF: 0.268 AC: 390790AN: 1457516Hom.: 55095 Cov.: 30 AF XY: 0.268 AC XY: 194275AN XY: 725298
GnomAD4 genome AF: 0.216 AC: 32867AN: 152158Hom.: 4288 Cov.: 32 AF XY: 0.219 AC XY: 16273AN XY: 74386
ClinVar
Submissions by phenotype
not specified Benign:2
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: Variant associated with alopecia, ankylosing spondylitis, hypertension in pregnancy, carotid atherosclerosis - dubious and not relevant to patient disease -
This variant is classified as Benign based on local population frequency. This variant was detected in 51% of patients studied by a panel of primary immunodeficiencies. Number of patients: 49. Only high quality variants are reported. -
Sterile multifocal osteomyelitis with periostitis and pustulosis Benign:2
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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:2
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This variant is associated with the following publications: (PMID: 17899305, 8641687, 19818512, 12624309, 11841485) -
Autoinflammatory syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at