rs4986958
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_005534.4(IFNGR2):c.173C>G(p.Thr58Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0131 in 1,614,056 control chromosomes in the GnomAD database, including 912 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. T58T) has been classified as Likely benign.
Frequency
Consequence
NM_005534.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IFNGR2 | NM_005534.4 | c.173C>G | p.Thr58Arg | missense_variant | 2/7 | ENST00000290219.11 | |
IFNGR2 | NM_001329128.2 | c.230C>G | p.Thr77Arg | missense_variant | 3/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IFNGR2 | ENST00000290219.11 | c.173C>G | p.Thr58Arg | missense_variant | 2/7 | 1 | NM_005534.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0463 AC: 7039AN: 152090Hom.: 458 Cov.: 32
GnomAD3 exomes AF: 0.0155 AC: 3900AN: 251482Hom.: 190 AF XY: 0.0124 AC XY: 1688AN XY: 135918
GnomAD4 exome AF: 0.00960 AC: 14039AN: 1461848Hom.: 452 Cov.: 32 AF XY: 0.00883 AC XY: 6425AN XY: 727224
GnomAD4 genome ? AF: 0.0463 AC: 7043AN: 152208Hom.: 460 Cov.: 32 AF XY: 0.0451 AC XY: 3360AN XY: 74428
ClinVar
Submissions by phenotype
Immunodeficiency 28 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Interferon gamma receptor deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing;curation | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Aug 18, 2011 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 09, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at