4-184421904-T-G

Variant names:

• chr4-184421904-T-G
• rs1425551
• NM_002199.4:c.88-2336A>C

Variant summary

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

The NM_002199.4(IRF2):​c.88-2336A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 152,026 control chromosomes in the GnomAD database, including 12,431 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 (12431 hom., cov: 31)
• Consequence: IRF2 NM_002199.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.541
• Publications: 12 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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IRF2	NM_002199.4	c.88-2336A>C		intron_variant	Intron 2 of 8	ENST00000393593.8	NP_002190.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IRF2	ENST00000393593.8	c.88-2336A>C		intron_variant	Intron 2 of 8	1	NM_002199.4	ENSP00000377218.3

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58438 AN: 151908 Hom.: 12430 Cov.: 31

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.384 AC: 58453 AN: 152026 Hom.: 12431 Cov.: 31 AF XY: 0.377 AC XY: 28012 AN XY: 74294

African (AFR) AF: 0.221 AC: 9166 AN: 41460

American (AMR) AF: 0.354 AC: 5414 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1343 AN: 3468

East Asian (EAS) AF: 0.167 AC: 865 AN: 5166

South Asian (SAS) AF: 0.417 AC: 2012 AN: 4826

European-Finnish (FIN) AF: 0.398 AC: 4199 AN: 10542

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34122 AN: 67968

Other (OTH) AF: 0.391 AC: 826 AN: 2112

Alfa AF: 0.460 Hom.: 9367

Bravo AF: 0.377

Asia WGS AF: 0.285 AC: 993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.0
DANN	Benign	0.34
PhyloP100		-0.54
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: rs1425551; hg19: chr4-185343058;