chr1-234607491-G-A

Variant names:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_182972.3(IRF2BP2):c.1410C>T(p.Gly470Gly) 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:3

Conservation

PhyloP100: 0.499

Publications

10 publications found

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 Gene-Disease associations (from GenCC):

immunodeficiency, common variable, 14
Inheritance: AD, Unknown Classification: LIMITED Submitted by: ClinGen, Ambry Genetics, Labcorp Genetics (formerly Invitae)

IRF2BP2 links:

ENSG00000228830 (HGNC:):

ENSG00000228830 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
IRF2BP2	NM_182972.3 link	c.1410C>T	p.Gly470Gly	synonymous_variant	Exon 2 of 2	ENST00000366609.4	NP_892017.2	Q7Z5L9-1
IRF2BP2	NM_001077397.1 link	c.1362C>T	p.Gly454Gly	synonymous_variant	Exon 2 of 2		NP_001070865.1	Q7Z5L9-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
IRF2BP2	ENST00000366609.4 link	c.1410C>T	p.Gly470Gly	synonymous_variant	Exon 2 of 2	1	NM_182972.3	ENSP00000355568.3	Q7Z5L9-1
IRF2BP2	ENST00000366610.8 link	c.1362C>T	p.Gly454Gly	synonymous_variant	Exon 2 of 2	1		ENSP00000355569.3	Q7Z5L9-2
IRF2BP2	ENST00000491430.1 link	n.423C>T		non_coding_transcript_exon_variant	Exon 2 of 2	1
ENSG00000228830	ENST00000436039.1 link	n.484G>A		non_coding_transcript_exon_variant	Exon 1 of 2	3

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

GnomAD2 exomes

AF:

0.108

AC:

27150

AN:

251370

AF XY:

0.110

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 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

African (AFR)

AF:

0.0899

AC:

3010

AN:

33480

American (AMR)

AF:

0.0615

AC:

2751

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.131

AC:

3431

AN:

26136

East Asian (EAS)

AF:

0.0198

AC:

787

AN:

39700

South Asian (SAS)

AF:

0.0797

AC:

6873

AN:

86258

European-Finnish (FIN)

AF:

0.133

AC:

7092

AN:

53406

Middle Eastern (MID)

AF:

0.154

AC:

889

AN:

5768

European-Non Finnish (NFE)

AF:

0.139

AC:

154989

AN:

1111996

Other (OTH)

AF:

0.117

AC:

7059

AN:

60394

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

11259

22518

33776

45035

56294

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.114

AC:

17428

AN:

152264

Hom.:

1100

Cov.:

AF XY:

0.112

AC XY:

8364

AN XY:

74448

show subpopulations

African (AFR)

AF:

0.0917

AC:

3812

AN:

41554

American (AMR)

AF:

0.0821

AC:

1256

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.127

AC:

440

AN:

3472

East Asian (EAS)

AF:

0.0258

AC:

134

AN:

5186

South Asian (SAS)

AF:

0.0700

AC:

338

AN:

4830

European-Finnish (FIN)

AF:

0.133

AC:

1415

AN:

10602

Middle Eastern (MID)

AF:

0.156

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.141

AC:

9607

AN:

68000

Other (OTH)

AF:

0.117

AC:

247

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

824

1647

2471

3294

4118

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.130

Hom.:

2297

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:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

not specified

Benign:1

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

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 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

(source)

DANN

Benign

0.88

PhyloP100

0.50

RBP_binding_hub_radar

0.92

RBP_regulation_power_radar

2.7

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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chr1-234607491-G-A

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over