rs11132242

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002199.4(IRF2):​c.530-1708T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 152,008 control chromosomes in the GnomAD database, including 9,437 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 0.35 ( 9437 hom., cov: 32)

Consequence

IRF2
NM_002199.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.101
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IRF2NM_002199.4 linkuse as main transcriptc.530-1708T>C intron_variant ENST00000393593.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IRF2ENST00000393593.8 linkuse as main transcriptc.530-1708T>C intron_variant 1 NM_002199.4 P1P14316-1

Frequencies

GnomAD3 genomes
AF:
0.350
AC:
53111
AN:
151892
Hom.:
9437
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.337
Gnomad AMI
AF:
0.469
Gnomad AMR
AF:
0.312
Gnomad ASJ
AF:
0.359
Gnomad EAS
AF:
0.301
Gnomad SAS
AF:
0.300
Gnomad FIN
AF:
0.319
Gnomad MID
AF:
0.443
Gnomad NFE
AF:
0.375
Gnomad OTH
AF:
0.344
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.350
AC:
53140
AN:
152008
Hom.:
9437
Cov.:
32
AF XY:
0.345
AC XY:
25609
AN XY:
74266
show subpopulations
Gnomad4 AFR
AF:
0.337
Gnomad4 AMR
AF:
0.311
Gnomad4 ASJ
AF:
0.359
Gnomad4 EAS
AF:
0.301
Gnomad4 SAS
AF:
0.300
Gnomad4 FIN
AF:
0.319
Gnomad4 NFE
AF:
0.375
Gnomad4 OTH
AF:
0.343
Alfa
AF:
0.368
Hom.:
13947
Bravo
AF:
0.350
Asia WGS
AF:
0.258
AC:
898
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
2.8
DANN
Benign
0.39

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs11132242; hg19: chr4-185321941; API