Variant rs8722 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_182972.3(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
NM_182972.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.511

Variant links:

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]

IRF2BP2 links:

(HGNC:):

links:

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	UniProt
IRF2BP2	NM_182972.3 linkuse as main transcript	c.991C>T	p.Leu331=	synonymous_variant	1/2	ENST00000366609.4
IRF2BP2	NM_001077397.1 linkuse as main transcript	c.991C>T	p.Leu331=	synonymous_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IRF2BP2	ENST00000366609.4 linkuse as main transcript	c.991C>T	p.Leu331=	synonymous_variant	1/2	1	NM_182972.3	P3	Q7Z5L9-1
IRF2BP2	ENST00000366610.7 linkuse as main transcript	c.991C>T	p.Leu331=	synonymous_variant	1/2	1		A1	Q7Z5L9-2
	ENST00000436039.1 linkuse as main transcript	n.630+867G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.167

AC:

25369

AN:

152106

Hom.:

2671

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0424

Gnomad AMI

AF:

0.242

Gnomad AMR

AF:

0.169

Gnomad ASJ

AF:

0.227

Gnomad EAS

AF:

0.210

Gnomad SAS

AF:

0.101

Gnomad FIN

AF:

0.255

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.225

Gnomad OTH

AF:

0.189

GnomAD3 exomes

AF:

0.189

AC:

45928

AN:

242520

Hom.:

4970

AF XY:

0.192

AC XY:

25291

AN XY:

131958

show subpopulations

Gnomad AFR exome

AF:

0.0345

Gnomad AMR exome

AF:

0.125

Gnomad ASJ exome

AF:

0.231

Gnomad EAS exome

AF:

0.204

Gnomad SAS exome

AF:

0.102

Gnomad FIN exome

AF:

0.255

Gnomad NFE exome

AF:

0.235

Gnomad OTH exome

AF:

0.208

GnomAD4 exome

AF:

0.216

AC:

315187

AN:

1456336

Hom.:

36171

Cov.:

AF XY:

0.213

AC XY:

154599

AN XY:

724136

show subpopulations

Gnomad4 AFR exome

AF:

0.0353

Gnomad4 AMR exome

AF:

0.130

Gnomad4 ASJ exome

AF:

0.229

Gnomad4 EAS exome

AF:

0.227

Gnomad4 SAS exome

AF:

0.101

Gnomad4 FIN exome

AF:

0.255

Gnomad4 NFE exome

AF:

0.233

Gnomad4 OTH exome

AF:

0.207

GnomAD4 genome

AF:

0.167

AC:

25361

AN:

152224

Hom.:

2668

Cov.:

AF XY:

0.167

AC XY:

12408

AN XY:

74406

show subpopulations

Gnomad4 AFR

AF:

0.0423

Gnomad4 AMR

AF:

0.168

Gnomad4 ASJ

AF:

0.227

Gnomad4 EAS

AF:

0.210

Gnomad4 SAS

AF:

0.100

Gnomad4 FIN

AF:

0.255

Gnomad4 NFE

AF:

0.225

Gnomad4 OTH

AF:

0.189

Alfa

AF:

0.210

Hom.:

5404

Bravo

AF:

0.158

Asia WGS

AF:

0.158

AC:

550

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

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:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

DANN

Benign

0.94

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.8

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over