Variant 1-234605171-C-CAGTTATAAT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_182972.3(IRF2BP2):c.*1965_*1966insATTATAACT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.72 ( 40922 hom., cov: 0)

Failed GnomAD Quality Control

Consequence

IRF2BP2
NM_182972.3 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.02

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.833 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.1965_1966insATTATAACT		3_prime_UTR_variant	2/2	ENST00000366609.4
IRF2BP2	NM_001077397.1 linkuse as main transcript	c.1965_1966insATTATAACT		3_prime_UTR_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IRF2BP2	ENST00000366609.4 linkuse as main transcript	c.1965_1966insATTATAACT		3_prime_UTR_variant	2/2	1	NM_182972.3	P3	Q7Z5L9-1
IRF2BP2	ENST00000366610.7 linkuse as main transcript	c.1965_1966insATTATAACT		3_prime_UTR_variant	2/2	1		A1	Q7Z5L9-2

Frequencies

GnomAD3 genomes

AF:

0.724

AC:

109687

AN:

151546

Hom.:

40877

Cov.:

show subpopulations

Gnomad AFR

AF:

0.840

Gnomad AMI

AF:

0.653

Gnomad AMR

AF:

0.619

Gnomad ASJ

AF:

0.740

Gnomad EAS

AF:

0.263

Gnomad SAS

AF:

0.461

Gnomad FIN

AF:

0.713

Gnomad MID

AF:

0.737

Gnomad NFE

AF:

0.732

Gnomad OTH

AF:

0.728

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AC:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

GnomAD4 genome

AF:

0.724

AC:

109784

AN:

151664

Hom.:

40922

Cov.:

AF XY:

0.713

AC XY:

52892

AN XY:

74132

show subpopulations

Gnomad4 AFR

AF:

0.841

Gnomad4 AMR

AF:

0.619

Gnomad4 ASJ

AF:

0.740

Gnomad4 EAS

AF:

0.263

Gnomad4 SAS

AF:

0.461

Gnomad4 FIN

AF:

0.713

Gnomad4 NFE

AF:

0.732

Gnomad4 OTH

AF:

0.725

Alfa

AF:

0.599

Hom.:

1152

Bravo

AF:

0.722

Asia WGS

AF:

0.426

AC:

1486

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over