chr14-23373323-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_022789.4(IL25):c.205C>T(p.Arg69Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00007 in 1,613,984 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_022789.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL25 | NM_172314.2 | c.157C>T | p.Arg53Cys | missense_variant | 2/3 | ENST00000397242.3 | NP_758525.1 | |
IL25 | NM_022789.4 | c.205C>T | p.Arg69Cys | missense_variant | 1/2 | NP_073626.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL25 | ENST00000397242.3 | c.157C>T | p.Arg53Cys | missense_variant | 2/3 | 1 | NM_172314.2 | ENSP00000380417 | P2 | |
IL25 | ENST00000329715.2 | c.205C>T | p.Arg69Cys | missense_variant | 1/2 | 1 | ENSP00000328111 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000168 AC: 42AN: 249808Hom.: 0 AF XY: 0.000170 AC XY: 23AN XY: 135100
GnomAD4 exome AF: 0.0000677 AC: 99AN: 1461802Hom.: 0 Cov.: 32 AF XY: 0.0000743 AC XY: 54AN XY: 727208
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 20, 2024 | The c.205C>T (p.R69C) alteration is located in exon 1 (coding exon 1) of the IL25 gene. This alteration results from a C to T substitution at nucleotide position 205, causing the arginine (R) at amino acid position 69 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at