rs9808753
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_005534.4(IFNGR2):c.191A>G(p.Gln64Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 1,613,674 control chromosomes in the GnomAD database, including 25,826 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 Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
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.191A>G | p.Gln64Arg | missense_variant | 2/7 | ENST00000290219.11 | |
IFNGR2 | NM_001329128.2 | c.248A>G | p.Gln83Arg | missense_variant | 3/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IFNGR2 | ENST00000290219.11 | c.191A>G | p.Gln64Arg | missense_variant | 2/7 | 1 | NM_005534.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.179 AC: 27172AN: 151944Hom.: 2855 Cov.: 32
GnomAD3 exomes AF: 0.196 AC: 49315AN: 251460Hom.: 5990 AF XY: 0.195 AC XY: 26440AN XY: 135914
GnomAD4 exome AF: 0.162 AC: 236766AN: 1461612Hom.: 22977 Cov.: 34 AF XY: 0.164 AC XY: 119584AN XY: 727134
GnomAD4 genome ? AF: 0.179 AC: 27172AN: 152062Hom.: 2849 Cov.: 32 AF XY: 0.182 AC XY: 13506AN XY: 74336
ClinVar
Submissions by phenotype
Immunodeficiency 28 Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 10, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jan 24, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 25% of patients studied by a panel of primary immunodeficiencies. Number of patients: 22. Only high quality variants are reported. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 09, 2021 | This variant is associated with the following publications: (PMID: 20952689, 25854761) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at