X-71107769-G-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The ENST00000374202.7(IL2RG):āc.1077C>Gā(p.Ala359=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000289 in 1,037,664 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Synonymous variant affecting the same amino acid position (i.e. A359A) has been classified as Likely benign.
Frequency
Consequence
ENST00000374202.7 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL2RG | NM_000206.3 | c.1077C>G | p.Ala359= | synonymous_variant | 8/8 | ENST00000374202.7 | NP_000197.1 | |
IL2RG | XM_047442089.1 | c.*197C>G | 3_prime_UTR_variant | 7/7 | XP_047298045.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL2RG | ENST00000374202.7 | c.1077C>G | p.Ala359= | synonymous_variant | 8/8 | 1 | NM_000206.3 | ENSP00000363318 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 112237Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34405 FAILED QC
GnomAD3 exomes AF: 0.0000225 AC: 3AN: 133341Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 42383
GnomAD4 exome AF: 0.00000289 AC: 3AN: 1037664Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 331780
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 112237Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34405
ClinVar
Submissions by phenotype
X-linked severe combined immunodeficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 18, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at