21-33403138-T-C

Variant names:

• chr21-33403138-T-C
• rs8126756
• NM_001329128.2:c.-406T>C

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001329128.2(IFNGR2):​c.-406T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 147,368 control chromosomes in the GnomAD database, including 5,871 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.24 (5868 hom., cov: 27)
  • Exomes 𝑓: 0.099 (3 hom.)
• Consequence: IFNGR2 NM_001329128.2 5_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.194
• Publications: 13 publications found

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]

IFNGR2 Gene-Disease associations (from GenCC):

• immunodeficiency 28

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• autosomal dominant mendelian susceptibility to mycobacterial diseases due to partial IFNgammaR2 deficiency

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• autosomal recessive Mendelian susceptibility to mycobacterial diseases due to complete IFNgammaR2 deficiency

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• autosomal recessive Mendelian susceptibility to mycobacterial diseases due to partial IFNgammaR2 deficiency

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ENSG00000289939 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BP6: Variant 21-33403138-T-C is Benign according to our data. Variant chr21-33403138-T-C is described in ClinVar as Benign. ClinVar VariationId is 1289403.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001329128.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFNGR2	NM_001329128.2		c.-406T>C		5_prime_UTR	Exon 1 of 8	NP_001316057.1	E7EUY1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFNGR2	ENST00000964419.1		c.-406T>C		upstream_gene	N/A	ENSP00000634478.1
	ENSG00000289939	ENST00000701889.2		n.*91T>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.244 AC: 35825 AN: 147100 Hom.: 5854 Cov.: 27

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.109

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.203

GnomAD4 exome AF: 0.0989 AC: 18 AN: 182 Hom.: 3 Cov.: 0 AF XY: 0.0820 AC XY: 10 AN XY: 122

African (AFR) AF: 0.500 AC: 3 AN: 6

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.0921 AC: 14 AN: 152

Other (OTH) AF: 0.00 AC: 0 AN: 4

GnomAD4 genome AF: 0.244 AC: 35865 AN: 147186 Hom.: 5868 Cov.: 27 AF XY: 0.245 AC XY: 17535 AN XY: 71690

African (AFR) AF: 0.456 AC: 18087 AN: 39672

American (AMR) AF: 0.178 AC: 2652 AN: 14918

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 440 AN: 3400

East Asian (EAS) AF: 0.422 AC: 2088 AN: 4952

South Asian (SAS) AF: 0.295 AC: 1346 AN: 4566

European-Finnish (FIN) AF: 0.195 AC: 1940 AN: 9966

Middle Eastern (MID) AF: 0.121 AC: 35 AN: 290

European-Non Finnish (NFE) AF: 0.132 AC: 8772 AN: 66492

Other (OTH) AF: 0.200 AC: 409 AN: 2046

Alfa AF: 0.176 Hom.: 437

Bravo AF: 0.252

Asia WGS AF: 0.358 AC: 1193 AN: 3340

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	7.3
DANN	Benign	0.36
PhyloP100		-0.19
PromoterAI		0.058	Neutral
Mutation Taster		=294/6	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs8126756; hg19: chr21-34775444; COSMIC: COSV51641381; COSMIC: COSV51641381;