chr4-184473956-G-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002199.4(IRF2):c.-7+423C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 152,112 control chromosomes in the GnomAD database, including 9,563 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 0.33 ( 9540 hom., cov: 30)
Exomes 𝑓: 0.36 ( 23 hom. )
Consequence
IRF2
NM_002199.4 intron
NM_002199.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.167
Publications
3 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]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.326 AC: 49513AN: 151662Hom.: 9532 Cov.: 30 show subpopulations
GnomAD3 genomes
AF:
AC:
49513
AN:
151662
Hom.:
Cov.:
30
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.358 AC: 119AN: 332Hom.: 23 Cov.: 0 AF XY: 0.359 AC XY: 84AN XY: 234 show subpopulations
GnomAD4 exome
AF:
AC:
119
AN:
332
Hom.:
Cov.:
0
AF XY:
AC XY:
84
AN XY:
234
show subpopulations
African (AFR)
AF:
AC:
1
AN:
12
American (AMR)
AF:
AC:
1
AN:
4
Ashkenazi Jewish (ASJ)
AF:
AC:
2
AN:
4
East Asian (EAS)
AF:
AC:
3
AN:
10
South Asian (SAS)
AF:
AC:
11
AN:
30
European-Finnish (FIN)
AF:
AC:
5
AN:
12
Middle Eastern (MID)
AF:
AC:
1
AN:
4
European-Non Finnish (NFE)
AF:
AC:
92
AN:
238
Other (OTH)
AF:
AC:
3
AN:
18
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.484
Heterozygous variant carriers
0
3
6
9
12
15
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.326 AC: 49533AN: 151780Hom.: 9540 Cov.: 30 AF XY: 0.329 AC XY: 24416AN XY: 74160 show subpopulations
GnomAD4 genome
AF:
AC:
49533
AN:
151780
Hom.:
Cov.:
30
AF XY:
AC XY:
24416
AN XY:
74160
show subpopulations
African (AFR)
AF:
AC:
4743
AN:
41398
American (AMR)
AF:
AC:
6850
AN:
15264
Ashkenazi Jewish (ASJ)
AF:
AC:
1326
AN:
3466
East Asian (EAS)
AF:
AC:
2485
AN:
5150
South Asian (SAS)
AF:
AC:
1694
AN:
4804
European-Finnish (FIN)
AF:
AC:
4226
AN:
10516
Middle Eastern (MID)
AF:
AC:
96
AN:
292
European-Non Finnish (NFE)
AF:
AC:
27055
AN:
67880
Other (OTH)
AF:
AC:
759
AN:
2104
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1566
3132
4699
6265
7831
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
490
980
1470
1960
2450
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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