rs138717312
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_005534.4(IFNGR2):c.234C>T(p.Asp78=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000492 in 1,613,996 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00034 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00051 ( 15 hom. )
Consequence
IFNGR2
NM_005534.4 synonymous
NM_005534.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.01
Genes affected
IFNGR2 (HGNC:5440): (interferon gamma receptor 2) This gene (IFNGR2) encodes the non-ligand-binding beta chain of the gamma interferon receptor. Human interferon-gamma receptor is a heterodimer of IFNGR1 and IFNGR2. Defects in IFNGR2 are a cause of mendelian susceptibility to mycobacterial disease (MSMD), also known as familial disseminated atypical mycobacterial infection. MSMD is a genetically heterogeneous disease with autosomal recessive, autosomal dominant or X-linked inheritance. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 21-33421507-C-T is Benign according to our data. Variant chr21-33421507-C-T is described in ClinVar as [Benign]. Clinvar id is 541803.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-3.01 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.000335 (51/152174) while in subpopulation SAS AF= 0.00767 (37/4826). AF 95% confidence interval is 0.00572. There are 1 homozygotes in gnomad4. There are 36 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAdExome4 at 15 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IFNGR2 | NM_005534.4 | c.234C>T | p.Asp78= | synonymous_variant | 3/7 | ENST00000290219.11 | |
IFNGR2 | NM_001329128.2 | c.291C>T | p.Asp97= | synonymous_variant | 4/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IFNGR2 | ENST00000290219.11 | c.234C>T | p.Asp78= | synonymous_variant | 3/7 | 1 | NM_005534.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000335 AC: 51AN: 152056Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.00105 AC: 264AN: 251446Hom.: 2 AF XY: 0.00126 AC XY: 171AN XY: 135888
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GnomAD4 exome AF: 0.000508 AC: 743AN: 1461822Hom.: 15 Cov.: 33 AF XY: 0.000686 AC XY: 499AN XY: 727216
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Immunodeficiency 28 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 14, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
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DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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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