11-117995681-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001558.4(IL10RA):c.781C>T(p.Arg261Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00031 in 1,613,900 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001558.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL10RA | NM_001558.4 | c.781C>T | p.Arg261Trp | missense_variant | 6/7 | ENST00000227752.8 | NP_001549.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL10RA | ENST00000227752.8 | c.781C>T | p.Arg261Trp | missense_variant | 6/7 | 1 | NM_001558.4 | ENSP00000227752 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000237 AC: 36AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000482 AC: 121AN: 251196Hom.: 0 AF XY: 0.000486 AC XY: 66AN XY: 135808
GnomAD4 exome AF: 0.000318 AC: 465AN: 1461620Hom.: 3 Cov.: 31 AF XY: 0.000325 AC XY: 236AN XY: 727114
GnomAD4 genome AF: 0.000236 AC: 36AN: 152280Hom.: 0 Cov.: 32 AF XY: 0.000228 AC XY: 17AN XY: 74466
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2023 | IL10RA: BP4 - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Sep 27, 2017 | The R261W variant in the IL10RA gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. This variant is observed in 43/10,152 alleles (0.4%) from individuals of Ashkenazi Jewish background, and 117/276,954 global alleles (0.04%), in large population cohorts (Lek et al., 2016). The R261W variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position where amino acids with similar properties to Arginine are tolerated across species. However, in silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. The R261W variant is reported as a variant of uncertain significance in ClinVar by different clinical laboratories, but additional evidence is not available (ClinVar SCV000297101.2, SCV000367434.2; Landrum et al., 2016). We also interpret R261W as a variant of uncertain significance. - |
Inflammatory bowel disease 28 Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 19, 2024 | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia | Oct 04, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at