1-206768644-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_000572.3(IL10):c.529C>T(p.Arg177*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000377 in 1,589,440 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000572.3 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL10 | NM_000572.3 | c.529C>T | p.Arg177* | stop_gained | Exon 5 of 5 | ENST00000423557.1 | NP_000563.1 | |
IL10 | NM_001382624.1 | c.274C>T | p.Arg92* | stop_gained | Exon 3 of 3 | NP_001369553.1 | ||
IL10 | NR_168466.1 | n.826C>T | non_coding_transcript_exon_variant | Exon 6 of 6 | ||||
IL10 | NR_168467.1 | n.356C>T | non_coding_transcript_exon_variant | Exon 3 of 3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152122Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250356Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135482
GnomAD4 exome AF: 0.00000209 AC: 3AN: 1437318Hom.: 0 Cov.: 26 AF XY: 0.00000140 AC XY: 1AN XY: 716502
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152122Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74306
ClinVar
Submissions by phenotype
Inflammatory bowel disease Uncertain:1
This sequence change creates a premature translational stop signal (p.Arg177*) in the IL10 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 2 amino acid(s) of the IL10 protein. This variant is present in population databases (rs142726516, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with IL10-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at