2-113132727-T-C
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_173842.3(IL1RN):c.390T>C(p.Ser130Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 1,614,016 control chromosomes in the GnomAD database, including 77,305 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
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.339 AC: 51496AN: 152098Hom.: 9523 Cov.: 33
GnomAD3 exomes AF: 0.305 AC: 76749AN: 251324Hom.: 13280 AF XY: 0.294 AC XY: 39936AN XY: 135834
GnomAD4 exome AF: 0.294 AC: 430010AN: 1461800Hom.: 67767 Cov.: 37 AF XY: 0.289 AC XY: 210490AN XY: 727216
GnomAD4 genome AF: 0.339 AC: 51534AN: 152216Hom.: 9538 Cov.: 33 AF XY: 0.339 AC XY: 25261AN XY: 74420
ClinVar
Submissions by phenotype
Sterile multifocal osteomyelitis with periostitis and pustulosis Benign:3
- -
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 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: Frequency -
This variant is classified as Benign based on local population frequency. This variant was detected in 48% of patients studied by a panel of primary immunodeficiencies. Number of patients: 46. Only high quality variants are reported. -
not provided Benign:2
- -
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at