1-206768666-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PP3_StrongBS2
The NM_000572.3(IL10):āc.507A>Cā(p.Glu169Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,608,174 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 (ā ).
Frequency
Consequence
NM_000572.3 missense
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.507A>C | p.Glu169Asp | missense_variant | Exon 5 of 5 | ENST00000423557.1 | NP_000563.1 | |
IL10 | NM_001382624.1 | c.252A>C | p.Glu84Asp | missense_variant | Exon 3 of 3 | NP_001369553.1 | ||
IL10 | NR_168466.1 | n.804A>C | non_coding_transcript_exon_variant | Exon 6 of 6 | ||||
IL10 | NR_168467.1 | n.334A>C | non_coding_transcript_exon_variant | Exon 3 of 3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249976Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135306
GnomAD4 exome AF: 0.0000124 AC: 18AN: 1455864Hom.: 0 Cov.: 28 AF XY: 0.0000110 AC XY: 8AN XY: 724686
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152310Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74484
ClinVar
Submissions by phenotype
Inflammatory bowel disease Uncertain:1
This sequence change replaces glutamic acid with aspartic acid at codon 169 of the IL10 protein (p.Glu169Asp). The glutamic acid residue is moderately conserved and there is a small physicochemical difference between glutamic acid and aspartic acid. This variant is present in population databases (rs568879359, ExAC 0.01%). This missense change has been observed in individual(s) with a primary immunodeficiency disorder (PMID: 30290665). ClinVar contains an entry for this variant (Variation ID: 939398). 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: "Probably Damaging"; Align-GVGD: "Class C0"). 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