chr2-213021923-A-ATTTTATCT

Position:

• chr2-213021923-A-ATTTTATCT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001387220.1(IKZF2):​c.712+69_712+70insAGATAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.54 (22913 hom., cov: 0)
  • Exomes 𝑓: 0.59 (233814 hom.)
• Consequence: IKZF2 NM_001387220.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.149

Genes affected

IKZF2 (HGNC:13177): (IKAROS family zinc finger 2) This gene encodes a member of the Ikaros family of zinc-finger proteins. Three members of this protein family (Ikaros, Aiolos and Helios) are hematopoietic-specific transcription factors involved in the regulation of lymphocyte development. This protein forms homo- or hetero-dimers with other Ikaros family members, and is thought to function predominantly in early hematopoietic development. Multiple transcript variants encoding different isoforms have been found for this gene, but the biological validity of some variants has not been determined. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 2-213021923-A-ATTTTATCT is Benign according to our data. Variant chr2-213021923-A-ATTTTATCT is described in ClinVar as [Benign]. Clinvar id is 2687988.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.773 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IKZF2	NM_001387220.1	c.712+69_712+70insAGATAAAA		intron_variant		ENST00000434687.6	NP_001374149.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IKZF2	ENST00000434687.6	c.712+69_712+70insAGATAAAA		intron_variant		5	NM_001387220.1	ENSP00000412869	P4

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81281 AN: 151208 Hom.: 22906 Cov.: 0

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.568

GnomAD4 exome AF: 0.594 AC: 771390 AN: 1298834 Hom.: 233814 Cov.: 20 AF XY: 0.596 AC XY: 382775 AN XY: 642278

Gnomad4 AFR exome AF: 0.346

Gnomad4 AMR exome AF: 0.709

Gnomad4 ASJ exome AF: 0.588

Gnomad4 EAS exome AF: 0.787

Gnomad4 SAS exome AF: 0.646

Gnomad4 FIN exome AF: 0.499

Gnomad4 NFE exome AF: 0.591

Gnomad4 OTH exome AF: 0.599

GnomAD4 genome AF: 0.537 AC: 81317 AN: 151326 Hom.: 22913 Cov.: 0 AF XY: 0.539 AC XY: 39836 AN XY: 73962

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.669

Gnomad4 ASJ AF: 0.577

Gnomad4 EAS AF: 0.793

Gnomad4 SAS AF: 0.630

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.590

Gnomad4 OTH AF: 0.565

Alfa AF: 0.533 Hom.: 2348

Bravo AF: 0.544

Asia WGS AF: 0.602 AC: 2092 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

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 76% of patients studied by a panel of primary immunodeficiencies. Number of patients: 72. Only high quality variants are reported. -

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: rs3830257; hg19: chr2-213886647;