chr12-68155252-TTTGA-T
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BS1_SupportingBS2
The NM_000619.3(IFNG):c.*97_*100del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00177 in 760,522 control chromosomes in the GnomAD database, including 9 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Genomes: 𝑓 0.0031 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0014 ( 8 hom. )
Consequence
IFNG
NM_000619.3 3_prime_UTR
NM_000619.3 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.908
Genes affected
IFNG (HGNC:5438): (interferon gamma) This gene encodes a soluble cytokine that is a member of the type II interferon class. The encoded protein is secreted by cells of both the innate and adaptive immune systems. The active protein is a homodimer that binds to the interferon gamma receptor which triggers a cellular response to viral and microbial infections. Mutations in this gene are associated with an increased susceptibility to viral, bacterial and parasitic infections and to several autoimmune diseases. [provided by RefSeq, Dec 2015]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BS1
Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00143 (869/608186) while in subpopulation MID AF= 0.0194 (50/2582). AF 95% confidence interval is 0.0151. There are 8 homozygotes in gnomad4_exome. There are 426 alleles in male gnomad4_exome subpopulation. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
BS2
High Homozygotes in GnomAdExome4 at 8 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IFNG | NM_000619.3 | c.*97_*100del | 3_prime_UTR_variant | 4/4 | ENST00000229135.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IFNG | ENST00000229135.4 | c.*97_*100del | 3_prime_UTR_variant | 4/4 | 1 | NM_000619.3 | P1 | ||
IFNG-AS1 | ENST00000536914.1 | n.337-79271_337-79268del | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00314 AC: 478AN: 152218Hom.: 1 Cov.: 32
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GnomAD4 exome AF: 0.00143 AC: 869AN: 608186Hom.: 8 AF XY: 0.00138 AC XY: 426AN XY: 309528
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GnomAD4 genome AF: 0.00314 AC: 479AN: 152336Hom.: 1 Cov.: 32 AF XY: 0.00294 AC XY: 219AN XY: 74506
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1Other:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Aplastic anemia Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not provided Other:1
not provided, no classification provided | literature only | Human Evolutionary Genetics, Institut Pasteur | - | - - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at