chr1-234605171-C-CAGTTATAAT

Position:

• chr1-234605171-C-CAGTTATAAT

Variant summary

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

The ENST00000366609.4(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 ENST00000366609.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.02

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]

ACMG classification

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	Protein	UniProt
IRF2BP2	NM_182972.3	c.*1965_*1966insATTATAACT		3_prime_UTR_variant	2/2	ENST00000366609.4	NP_892017.2
IRF2BP2	NM_001077397.1	c.*1965_*1966insATTATAACT		3_prime_UTR_variant	2/2		NP_001070865.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IRF2BP2	ENST00000366609.4	c.*1965_*1966insATTATAACT		3_prime_UTR_variant	2/2	1	NM_182972.3	ENSP00000355568	P3
IRF2BP2	ENST00000366610.7	c.*1965_*1966insATTATAACT		3_prime_UTR_variant	2/2	1		ENSP00000355569	A1

Frequencies

GnomAD3 genomes AF: 0.724 AC: 109687 AN: 151546 Hom.: 40877 Cov.: 0

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: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.724 AC: 109784 AN: 151664 Hom.: 40922 Cov.: 0 AF XY: 0.713 AC XY: 52892 AN XY: 74132

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

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3045215; hg19: chr1-234740917;