rs9376267
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000416.3(IFNGR1):c.86-2817G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 398,504 control chromosomes in the GnomAD database, including 13,598 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.23 ( 4593 hom., cov: 32)
Exomes 𝑓: 0.26 ( 9005 hom. )
Consequence
IFNGR1
NM_000416.3 intron
NM_000416.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.151
Genes affected
IFNGR1 (HGNC:5439): (interferon gamma receptor 1) This gene (IFNGR1) encodes the ligand-binding chain (alpha) of the gamma interferon receptor. Human interferon-gamma receptor is a heterodimer of IFNGR1 and IFNGR2. A genetic variation in IFNGR1 is associated with susceptibility to Helicobacter pylori infection. In addition, defects in IFNGR1 are a cause of mendelian susceptibility to mycobacterial disease, also known as familial disseminated atypical mycobacterial infection. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant 6-137209894-C-T is Benign according to our data. Variant chr6-137209894-C-T is described in ClinVar as [Benign]. Clinvar id is 2688425.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IFNGR1 | NM_000416.3 | c.86-2817G>A | intron_variant | ENST00000367739.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IFNGR1 | ENST00000367739.9 | c.86-2817G>A | intron_variant | 1 | NM_000416.3 | P2 |
Frequencies
GnomAD3 genomes AF: 0.230 AC: 35035AN: 152054Hom.: 4576 Cov.: 32
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GnomAD4 exome AF: 0.260 AC: 64120AN: 246332Hom.: 9005 Cov.: 0 AF XY: 0.261 AC XY: 32547AN XY: 124834
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GnomAD4 genome AF: 0.231 AC: 35092AN: 152172Hom.: 4593 Cov.: 32 AF XY: 0.238 AC XY: 17720AN XY: 74384
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
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 45% of patients studied by a panel of primary immunodeficiencies. Number of patients: 40. Only high quality variants are reported. - |
Computational scores
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Benign
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DANN
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at