11-117986504-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001558.4(IL10RA):c.37C>T(p.Leu13Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001558.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL10RA | NM_001558.4 | c.37C>T | p.Leu13Phe | missense_variant | Exon 1 of 7 | ENST00000227752.8 | NP_001549.2 | |
IL10RA | XM_047426882.1 | c.-303C>T | 5_prime_UTR_variant | Exon 1 of 7 | XP_047282838.1 | |||
IL10RA | NR_026691.2 | n.111C>T | non_coding_transcript_exon_variant | Exon 1 of 8 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1404196Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 693228
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Inflammatory bowel disease 28 Uncertain:1
ClinVar contains an entry for this variant (Variation ID: 1036326). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Not Available"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals affected with IL10RA-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces leucine, which is neutral and non-polar, with phenylalanine, which is neutral and non-polar, at codon 13 of the IL10RA protein (p.Leu13Phe). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at