rs2228145
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000565.4(IL6R):c.1073A>C(p.Asp358Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 1,604,538 control chromosomes in the GnomAD database, including 122,631 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D358Y) has been classified as Uncertain significance.
Frequency
Consequence
NM_000565.4 missense
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 |
---|---|---|---|---|---|---|---|
IL6R | NM_000565.4 | c.1073A>C | p.Asp358Ala | missense_variant | 9/10 | ENST00000368485.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL6R | ENST00000368485.8 | c.1073A>C | p.Asp358Ala | missense_variant | 9/10 | 1 | NM_000565.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.321 AC: 48587AN: 151302Hom.: 9020 Cov.: 30
GnomAD3 exomes AF: 0.379 AC: 94659AN: 249648Hom.: 19150 AF XY: 0.376 AC XY: 50669AN XY: 134926
GnomAD4 exome AF: 0.390 AC: 565992AN: 1453118Hom.: 113611 Cov.: 30 AF XY: 0.387 AC XY: 279734AN XY: 723282
GnomAD4 genome AF: 0.321 AC: 48588AN: 151420Hom.: 9020 Cov.: 30 AF XY: 0.317 AC XY: 23400AN XY: 73922
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jan 24, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 82% of patients studied by a panel of primary immunodeficiencies. Number of patients: 72. Only high quality variants are reported. - |
IL6R-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Interleukin 6, serum level of, quantitative trait locus Other:1
association, no assertion criteria provided | literature only | OMIM | Apr 01, 2007 | - - |
Soluble interleukin-6 receptor, serum level of, quantitative trait locus Other:1
association, no assertion criteria provided | literature only | OMIM | Apr 01, 2007 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at