rs7543281

Variant summary

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

The NM_182972.3(IRF2BP2):c.1410C>T(p.Gly470=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 1,614,126 control chromosomes in the GnomAD database, including 13,754 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 1100 hom., cov: 33)

Exomes 𝑓: 0.13 ( 12654 hom. )

Consequence

IRF2BP2
NM_182972.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.499

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=-0.58).

BP6

Variant 1-234607491-G-A is Benign according to our data. Variant chr1-234607491-G-A is described in ClinVar as [Benign]. Clinvar id is 402981.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.499 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.139 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.1410C>T	p.Gly470=	synonymous_variant	2/2	ENST00000366609.4
IRF2BP2	NM_001077397.1 linkuse as main transcript	c.1362C>T	p.Gly454=	synonymous_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IRF2BP2	ENST00000366609.4 linkuse as main transcript	c.1410C>T	p.Gly470=	synonymous_variant	2/2	1	NM_182972.3	P3	Q7Z5L9-1
IRF2BP2	ENST00000366610.7 linkuse as main transcript	c.1362C>T	p.Gly454=	synonymous_variant	2/2	1		A1	Q7Z5L9-2
	ENST00000436039.1 linkuse as main transcript	n.484G>A		non_coding_transcript_exon_variant	1/2	3
IRF2BP2	ENST00000491430.1 linkuse as main transcript	n.423C>T		non_coding_transcript_exon_variant	2/2	1

Frequencies

GnomAD3 genomes

AF:

0.115

AC:

17430

AN:

152146

Hom.:

1101

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0918

Gnomad AMI

AF:

0.146

Gnomad AMR

AF:

0.0822

Gnomad ASJ

AF:

0.127

Gnomad EAS

AF:

0.0260

Gnomad SAS

AF:

0.0699

Gnomad FIN

AF:

0.133

Gnomad MID

AF:

0.171

Gnomad NFE

AF:

0.141

Gnomad OTH

AF:

0.118

GnomAD3 exomes

AF:

0.108

AC:

27150

AN:

251370

Hom.:

1659

AF XY:

0.110

AC XY:

14984

AN XY:

135860

show subpopulations

Gnomad AFR exome

AF:

0.0908

Gnomad AMR exome

AF:

0.0586

Gnomad ASJ exome

AF:

0.134

Gnomad EAS exome

AF:

0.0262

Gnomad SAS exome

AF:

0.0802

Gnomad FIN exome

AF:

0.130

Gnomad NFE exome

AF:

0.139

Gnomad OTH exome

AF:

0.119

GnomAD4 exome

AF:

0.128

AC:

186881

AN:

1461862

Hom.:

12654

Cov.:

AF XY:

0.127

AC XY:

92252

AN XY:

727232

show subpopulations

Gnomad4 AFR exome

AF:

0.0899

Gnomad4 AMR exome

AF:

0.0615

Gnomad4 ASJ exome

AF:

0.131

Gnomad4 EAS exome

AF:

0.0198

Gnomad4 SAS exome

AF:

0.0797

Gnomad4 FIN exome

AF:

0.133

Gnomad4 NFE exome

AF:

0.139

Gnomad4 OTH exome

AF:

0.117

GnomAD4 genome

AF:

0.114

AC:

17428

AN:

152264

Hom.:

1100

Cov.:

AF XY:

0.112

AC XY:

8364

AN XY:

74448

show subpopulations

Gnomad4 AFR

AF:

0.0917

Gnomad4 AMR

AF:

0.0821

Gnomad4 ASJ

AF:

0.127

Gnomad4 EAS

AF:

0.0258

Gnomad4 SAS

AF:

0.0700

Gnomad4 FIN

AF:

0.133

Gnomad4 NFE

AF:

0.141

Gnomad4 OTH

AF:

0.117

Alfa

AF:

0.134

Hom.:

1747

Bravo

AF:

0.108

Asia WGS

AF:

0.0530

AC:

184

AN:

3478

EpiCase

AF:

0.137

EpiControl

AF:

0.140

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

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: MAF -

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

-0.58

Cadd

Benign

Dann

Benign

0.88

RBP_binding_hub_radar

0.92

RBP_regulation_power_radar

2.7

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