rs8722
Positions:
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The ENST00000366609.4(IRF2BP2):c.991C>T(p.Leu331=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 1,608,560 control chromosomes in the GnomAD database, including 38,839 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.17 ( 2668 hom., cov: 33)
Exomes 𝑓: 0.22 ( 36171 hom. )
Consequence
IRF2BP2
ENST00000366609.4 synonymous
ENST00000366609.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.511
Genes affected
IRF2BP2 (HGNC:21729): (interferon regulatory factor 2 binding protein 2) This gene encodes an interferon regulatory factor-2 (IRF2) binding protein that interacts with the C-terminal transcriptional repression domain of IRF2. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP6
Variant 1-234608504-G-A is Benign according to our data. Variant chr1-234608504-G-A is described in ClinVar as [Benign]. Clinvar id is 402982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.511 with no splicing effect.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IRF2BP2 | NM_182972.3 | c.991C>T | p.Leu331= | synonymous_variant | 1/2 | ENST00000366609.4 | NP_892017.2 | |
IRF2BP2 | NM_001077397.1 | c.991C>T | p.Leu331= | synonymous_variant | 1/2 | NP_001070865.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IRF2BP2 | ENST00000366609.4 | c.991C>T | p.Leu331= | synonymous_variant | 1/2 | 1 | NM_182972.3 | ENSP00000355568 | P3 | |
IRF2BP2 | ENST00000366610.7 | c.991C>T | p.Leu331= | synonymous_variant | 1/2 | 1 | ENSP00000355569 | A1 | ||
ENST00000436039.1 | n.630+867G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.167 AC: 25369AN: 152106Hom.: 2671 Cov.: 33
GnomAD3 genomes
AF:
AC:
25369
AN:
152106
Hom.:
Cov.:
33
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:
GnomAD3 exomes AF: 0.189 AC: 45928AN: 242520Hom.: 4970 AF XY: 0.192 AC XY: 25291AN XY: 131958
GnomAD3 exomes
AF:
AC:
45928
AN:
242520
Hom.:
AF XY:
AC XY:
25291
AN XY:
131958
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.216 AC: 315187AN: 1456336Hom.: 36171 Cov.: 32 AF XY: 0.213 AC XY: 154599AN XY: 724136
GnomAD4 exome
AF:
AC:
315187
AN:
1456336
Hom.:
Cov.:
32
AF XY:
AC XY:
154599
AN XY:
724136
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.167 AC: 25361AN: 152224Hom.: 2668 Cov.: 33 AF XY: 0.167 AC XY: 12408AN XY: 74406
GnomAD4 genome
AF:
AC:
25361
AN:
152224
Hom.:
Cov.:
33
AF XY:
AC XY:
12408
AN XY:
74406
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
550
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jan 24, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 33% of patients studied by a panel of primary immunodeficiencies. Number of patients: 31. Only high quality variants are reported. - |
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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