chr4-122456312-C-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_000586.4(IL2):c.129G>T(p.Met43Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000244 in 1,610,242 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000586.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL2 | NM_000586.4 | c.129G>T | p.Met43Ile | missense_variant | 1/4 | ENST00000226730.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL2 | ENST00000226730.5 | c.129G>T | p.Met43Ile | missense_variant | 1/4 | 1 | NM_000586.4 | P1 | |
IL2 | ENST00000477645.1 | n.129G>T | non_coding_transcript_exon_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00132 AC: 201AN: 151934Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000353 AC: 88AN: 249132Hom.: 1 AF XY: 0.000319 AC XY: 43AN XY: 134726
GnomAD4 exome AF: 0.000130 AC: 189AN: 1458190Hom.: 0 Cov.: 29 AF XY: 0.000119 AC XY: 86AN XY: 725522
GnomAD4 genome AF: 0.00134 AC: 204AN: 152052Hom.: 1 Cov.: 32 AF XY: 0.00125 AC XY: 93AN XY: 74350
ClinVar
Submissions by phenotype
IL2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 31, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at