21-33247808-T-C

Variant names:

• chr21-33247808-T-C
• rs2834160
• NM_001289125.3:c.395-901T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001289125.3(IFNAR2):​c.395-901T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,226 control chromosomes in the GnomAD database, including 1,954 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.15 (1954 hom., cov: 31)
• Consequence: IFNAR2 NM_001289125.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.758
• Publications: 9 publications found

Genes affected

IFNAR2 (HGNC:5433): (interferon alpha and beta receptor subunit 2) The protein encoded by this gene is a type I membrane protein that forms one of the two chains of a receptor for interferons alpha and beta. Binding and activation of the receptor stimulates Janus protein kinases, which in turn phosphorylate several proteins, including STAT1 and STAT2. The protein belongs to the type II cytokine receptor family. Mutations in this gene are associated with Immunodeficiency 45. [provided by RefSeq, Jul 2020]

IFNAR2 Gene-Disease associations (from GenCC):

• immunodeficiency 45

  Inheritance: AR Classification: STRONG, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)

IFNAR2-IL10RB (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001289125.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFNAR2	NM_001289125.3	MANE Select	c.395-901T>C		intron	N/A	NP_001276054.1
	IFNAR2-IL10RB	NM_001414505.1		c.395-901T>C		intron	N/A	NP_001401434.1
	IFNAR2	NM_207585.3		c.395-901T>C		intron	N/A	NP_997468.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFNAR2	ENST00000342136.9	TSL:1 MANE Select	c.395-901T>C		intron	N/A	ENSP00000343957.5
	IFNAR2-IL10RB	ENST00000433395.7	TSL:5	c.395-901T>C		intron	N/A	ENSP00000388223.3
	IFNAR2	ENST00000382264.7	TSL:1	c.395-901T>C		intron	N/A	ENSP00000371699.3

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23203 AN: 152108 Hom.: 1953 Cov.: 31

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0530

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.144

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.152 AC: 23210 AN: 152226 Hom.: 1954 Cov.: 31 AF XY: 0.147 AC XY: 10972 AN XY: 74432

African (AFR) AF: 0.160 AC: 6641 AN: 41528

American (AMR) AF: 0.126 AC: 1923 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 446 AN: 3468

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5190

South Asian (SAS) AF: 0.0531 AC: 256 AN: 4824

European-Finnish (FIN) AF: 0.105 AC: 1116 AN: 10606

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12398 AN: 68006

Other (OTH) AF: 0.143 AC: 303 AN: 2114

Alfa AF: 0.169 Hom.: 5064

Bravo AF: 0.154

Asia WGS AF: 0.0300 AC: 105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.42
PhyloP100		-0.76
Mutation Taster		=100/0	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: rs2834160; hg19: chr21-34620113;