1-206770914-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_153758.5(IL19):c.-313C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000115 in 1,614,054 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_153758.5 5_prime_UTR_premature_start_codon_gain
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 |
---|---|---|---|---|---|---|---|---|
IL19 | NM_153758.5 | c.-313C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 7 | ENST00000659997.3 | NP_715639.2 | ||
IL10 | NM_000572.3 | c.371G>A | p.Arg124Gln | missense_variant | Exon 3 of 5 | ENST00000423557.1 | NP_000563.1 | |
IL19 | NM_153758.5 | c.-313C>T | 5_prime_UTR_variant | Exon 1 of 7 | ENST00000659997.3 | NP_715639.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL19 | ENST00000659997 | c.-313C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 7 | NM_153758.5 | ENSP00000499459.2 | ||||
IL10 | ENST00000423557.1 | c.371G>A | p.Arg124Gln | missense_variant | Exon 3 of 5 | 1 | NM_000572.3 | ENSP00000412237.1 | ||
IL19 | ENST00000659997 | c.-313C>T | 5_prime_UTR_variant | Exon 1 of 7 | NM_153758.5 | ENSP00000499459.2 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152148Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000119 AC: 30AN: 251402Hom.: 0 AF XY: 0.000169 AC XY: 23AN XY: 135878
GnomAD4 exome AF: 0.000120 AC: 176AN: 1461788Hom.: 1 Cov.: 35 AF XY: 0.000116 AC XY: 84AN XY: 727206
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152266Hom.: 0 Cov.: 31 AF XY: 0.0000671 AC XY: 5AN XY: 74462
ClinVar
Submissions by phenotype
Inflammatory bowel disease Uncertain:1
This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 124 of the IL10 protein (p.Arg124Gln). This variant is present in population databases (rs201365412, gnomAD 0.1%). This variant has not been reported in the literature in individuals affected with IL10-related conditions. ClinVar contains an entry for this variant (Variation ID: 1432945). An algorithm developed to predict the effect of missense changes on protein structure and function outputs the following: PolyPhen-2: "Benign". The glutamine 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