rs9684244

Variant names:

• chr4-184435091-G-C
• rs9684244
• NM_002199.4:c.-6-6021C>G

Your query was ambiguous. Multiple possible variants found:

• chr4-184435091-G-C
• chr4-184435091-G-T

Variant summary

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

The NM_002199.4(IRF2):​c.-6-6021C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 151,924 control chromosomes in the GnomAD database, including 11,083 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 0.38 (11083 hom., cov: 32)
• Consequence: IRF2 NM_002199.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690
• Publications: 6 publications found

Genes affected

IRF2 (HGNC:6117): (interferon regulatory factor 2) IRF2 encodes interferon regulatory factor 2, a member of the interferon regulatory transcription factor (IRF) family. IRF2 competitively inhibits the IRF1-mediated transcriptional activation of interferons alpha and beta, and presumably other genes that employ IRF1 for transcription activation. However, IRF2 also functions as a transcriptional activator of histone H4. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002199.4. 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
	IRF2	NM_002199.4	MANE Select	c.-6-6021C>G		intron	N/A	NP_002190.2	P14316-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IRF2	ENST00000393593.8	TSL:1 MANE Select	c.-6-6021C>G		intron	N/A	ENSP00000377218.3	P14316-1
	IRF2	ENST00000505067.6	TSL:3	c.-6-6021C>G		intron	N/A	ENSP00000421927.2	K4DIA4
	IRF2	ENST00000883917.1		c.-6-6021C>G		intron	N/A	ENSP00000553976.1

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57593 AN: 151806 Hom.: 11067 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.379 AC: 57646 AN: 151924 Hom.: 11083 Cov.: 32 AF XY: 0.382 AC XY: 28335 AN XY: 74242

African (AFR) AF: 0.363 AC: 15044 AN: 41438

American (AMR) AF: 0.481 AC: 7351 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1322 AN: 3460

East Asian (EAS) AF: 0.438 AC: 2258 AN: 5160

South Asian (SAS) AF: 0.387 AC: 1867 AN: 4822

European-Finnish (FIN) AF: 0.343 AC: 3608 AN: 10534

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.367 AC: 24932 AN: 67932

Other (OTH) AF: 0.384 AC: 809 AN: 2106

Alfa AF: 0.239 Hom.: 527

Bravo AF: 0.390

Asia WGS AF: 0.402 AC: 1397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.71
PhyloP100		0.069
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: rs9684244; hg19: chr4-185356245;