chr14-23373272-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_022789.4(IL25):c.154C>A(p.Leu52Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,868 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL25 | NM_172314.2 | c.106C>A | p.Leu36Met | missense_variant | 2/3 | ENST00000397242.3 | NP_758525.1 | |
IL25 | NM_022789.4 | c.154C>A | p.Leu52Met | missense_variant | 1/2 | NP_073626.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL25 | ENST00000397242.3 | c.106C>A | p.Leu36Met | missense_variant | 2/3 | 1 | NM_172314.2 | ENSP00000380417 | P2 | |
IL25 | ENST00000329715.2 | c.154C>A | p.Leu52Met | missense_variant | 1/2 | 1 | ENSP00000328111 | A2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461868Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727240
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 14, 2024 | The c.154C>A (p.L52M) alteration is located in exon 1 (coding exon 1) of the IL25 gene. This alteration results from a C to A substitution at nucleotide position 154, causing the leucine (L) at amino acid position 52 to be replaced by a methionine (M). 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
Publications
No publications associated with this variant yet.