11-117986480-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001558.4(IL10RA):c.13C>T(p.Leu5Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000045 in 1,555,628 control chromosomes in the GnomAD database, with no homozygous occurrence. 12/21 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.13C>T | p.Leu5Phe | missense_variant | Exon 1 of 7 | ENST00000227752.8 | NP_001549.2 | |
IL10RA | XM_047426882.1 | c.-327C>T | 5_prime_UTR_variant | Exon 1 of 7 | XP_047282838.1 | |||
IL10RA | NR_026691.2 | n.87C>T | non_coding_transcript_exon_variant | Exon 1 of 8 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152218Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000214 AC: 3AN: 1403410Hom.: 0 Cov.: 31 AF XY: 0.00000144 AC XY: 1AN XY: 692804
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152218Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74356
ClinVar
Submissions by phenotype
Inflammatory bowel disease 28 Uncertain:1
ClinVar contains an entry for this variant (Variation ID: 2182429). 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. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals affected with IL10RA-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.006%). This sequence change replaces leucine, which is neutral and non-polar, with phenylalanine, which is neutral and non-polar, at codon 5 of the IL10RA protein (p.Leu5Phe). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at