rs17175350
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000416.3(IFNGR1):āc.1004A>Cā(p.His335Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000787 in 1,614,194 control chromosomes in the GnomAD database, including 7 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 (ā ā ).
Frequency
Consequence
NM_000416.3 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IFNGR1 | NM_000416.3 | c.1004A>C | p.His335Pro | missense_variant | 7/7 | ENST00000367739.9 | NP_000407.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IFNGR1 | ENST00000367739.9 | c.1004A>C | p.His335Pro | missense_variant | 7/7 | 1 | NM_000416.3 | ENSP00000356713 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00392 AC: 597AN: 152210Hom.: 4 Cov.: 31
GnomAD3 exomes AF: 0.00107 AC: 269AN: 251328Hom.: 2 AF XY: 0.000729 AC XY: 99AN XY: 135844
GnomAD4 exome AF: 0.000461 AC: 674AN: 1461866Hom.: 3 Cov.: 32 AF XY: 0.000393 AC XY: 286AN XY: 727236
GnomAD4 genome AF: 0.00392 AC: 597AN: 152328Hom.: 4 Cov.: 31 AF XY: 0.00376 AC XY: 280AN XY: 74498
ClinVar
Submissions by phenotype
Disseminated atypical mycobacterial infection Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 25, 2024 | - - |
Mycobacterium tuberculosis, susceptibility to;C1838332:Helicobacter pylori infection, susceptibility to;C1864880:Hepatitis B virus, susceptibility to;C4011949:Immunodeficiency 27A;C4014863:Autosomal dominant mendelian susceptibility to mycobacterial diseases due to partial IFNgammaR1 deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Apr 26, 2022 | - - |
Interferon gamma receptor deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Aug 18, 2011 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2022 | IFNGR1: BP4, BS1, BS2 - |
Immunodeficiency 27A Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Sep 05, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at