chr4-184415698-T-C

Variant names:

• chr4-184415698-T-C
• rs7677486
• NM_002199.4:c.411+2469A>G

Variant summary

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

The NM_002199.4(IRF2):​c.411+2469A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 152,132 control chromosomes in the GnomAD database, including 18,477 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 0.48 (18477 hom., cov: 32)
• Consequence: IRF2 NM_002199.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.60

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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IRF2	NM_002199.4	c.411+2469A>G		intron_variant	Intron 5 of 8	ENST00000393593.8	NP_002190.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IRF2	ENST00000393593.8	c.411+2469A>G		intron_variant	Intron 5 of 8	1	NM_002199.4	ENSP00000377218.3

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72532 AN: 152014 Hom.: 18463 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.477 AC: 72577 AN: 152132 Hom.: 18477 Cov.: 32 AF XY: 0.469 AC XY: 34906 AN XY: 74376

African (AFR) AF: 0.329 AC: 13637 AN: 41496

American (AMR) AF: 0.458 AC: 7006 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1815 AN: 3472

East Asian (EAS) AF: 0.199 AC: 1033 AN: 5190

South Asian (SAS) AF: 0.419 AC: 2024 AN: 4826

European-Finnish (FIN) AF: 0.489 AC: 5162 AN: 10554

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.591 AC: 40198 AN: 67984

Other (OTH) AF: 0.490 AC: 1035 AN: 2114

Alfa AF: 0.555 Hom.: 102423

Bravo AF: 0.473

Asia WGS AF: 0.307 AC: 1072 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.011
DANN	Benign	0.29
PhyloP100		-2.6
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

Publications

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Other links and lift over

dbSNP: rs7677486; hg19: chr4-185336852;