1-206768652-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_000572.3(IL10):c.521T>C(p.Met174Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000375 in 1,601,478 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000572.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL10 | NM_000572.3 | c.521T>C | p.Met174Thr | missense_variant | 5/5 | ENST00000423557.1 | |
IL10 | NM_001382624.1 | c.266T>C | p.Met89Thr | missense_variant | 3/3 | ||
IL10 | NR_168466.1 | n.818T>C | non_coding_transcript_exon_variant | 6/6 | |||
IL10 | NR_168467.1 | n.348T>C | non_coding_transcript_exon_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL10 | ENST00000423557.1 | c.521T>C | p.Met174Thr | missense_variant | 5/5 | 1 | NM_000572.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152106Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250314Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135464
GnomAD4 exome AF: 0.00000345 AC: 5AN: 1449372Hom.: 0 Cov.: 27 AF XY: 0.00000277 AC XY: 2AN XY: 721892
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152106Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74302
ClinVar
Submissions by phenotype
Inflammatory bowel disease Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 31, 2021 | This sequence change replaces methionine with threonine at codon 174 of the IL10 protein (p.Met174Thr). The methionine residue is weakly conserved and there is a moderate physicochemical difference between methionine and threonine. This variant is present in population databases (rs762496248, ExAC 0.02%). This variant has not been reported in the literature in individuals affected with IL10-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The threonine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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