Variant chr2-213008144-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001387220.1(IKZF2):c.857-60T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 1,473,000 control chromosomes in the GnomAD database, including 43,970 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.22 ( 4043 hom., cov: 31)

Exomes 𝑓: 0.24 ( 39927 hom. )

Consequence

IKZF2
NM_001387220.1 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.765

Variant links:

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]

IKZF2 links:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 2-213008144-A-C is Benign according to our data. Variant chr2-213008144-A-C is described in ClinVar as [Benign]. Clinvar id is 2688165.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IKZF2	NM_001387220.1 linkuse as main transcript	c.857-60T>G		intron_variant		ENST00000434687.6	NP_001374149.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IKZF2	ENST00000434687.6 linkuse as main transcript	c.857-60T>G		intron_variant		5	NM_001387220.1	ENSP00000412869	P4	Q9UKS7-1
	ENST00000415387.1 linkuse as main transcript	n.81+13321T>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.220

AC:

33288

AN:

151200

Hom.:

4039

Cov.:

show subpopulations

Gnomad AFR

AF:

0.193

Gnomad AMI

AF:

0.193

Gnomad AMR

AF:

0.167

Gnomad ASJ

AF:

0.290

Gnomad EAS

AF:

0.00213

Gnomad SAS

AF:

0.0656

Gnomad FIN

AF:

0.283

Gnomad MID

AF:

0.239

Gnomad NFE

AF:

0.263

Gnomad OTH

AF:

0.220

GnomAD4 exome

AF:

0.236

AC:

311948

AN:

1321696

Hom.:

39927

AF XY:

0.232

AC XY:

150102

AN XY:

646742

show subpopulations

Gnomad4 AFR exome

AF:

0.194

Gnomad4 AMR exome

AF:

0.133

Gnomad4 ASJ exome

AF:

0.272

Gnomad4 EAS exome

AF:

0.00142

Gnomad4 SAS exome

AF:

0.0765

Gnomad4 FIN exome

AF:

0.291

Gnomad4 NFE exome

AF:

0.256

Gnomad4 OTH exome

AF:

0.218

GnomAD4 genome

AF:

0.220

AC:

33294

AN:

151304

Hom.:

4043

Cov.:

AF XY:

0.214

AC XY:

15815

AN XY:

73842

show subpopulations

Gnomad4 AFR

AF:

0.193

Gnomad4 AMR

AF:

0.167

Gnomad4 ASJ

AF:

0.290

Gnomad4 EAS

AF:

0.00213

Gnomad4 SAS

AF:

0.0660

Gnomad4 FIN

AF:

0.283

Gnomad4 NFE

AF:

0.263

Gnomad4 OTH

AF:

0.218

Alfa

AF:

0.243

Hom.:

615

Bravo

AF:

0.212

Asia WGS

AF:

0.0550

AC:

193

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

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 43% of patients studied by a panel of primary immunodeficiencies. Number of patients: 41. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.2

DANN

Benign

0.52

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