rs11980379

chr7-50402283-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006060.6(IKZF1):c.*1656T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 230,314 control chromosomes in the GnomAD database, including 7,130 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.25 (4810 hom., cov: 33)
  • Exomes 𝑓: 0.23 (2320 hom.)
• Consequence: IKZF1 NM_006060.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181

Genes affected

IKZF1 (HGNC:13176): (IKAROS family zinc finger 1) This gene encodes a transcription factor that belongs to the family of zinc-finger DNA-binding proteins associated with chromatin remodeling. The expression of this protein is restricted to the fetal and adult hemo-lymphopoietic system, and it functions as a regulator of lymphocyte differentiation. Several alternatively spliced transcript variants encoding different isoforms have been described for this gene. Most isoforms share a common C-terminal domain, which contains two zinc finger motifs that are required for hetero- or homo-dimerization, and for interactions with other proteins. The isoforms, however, differ in the number of N-terminal zinc finger motifs that bind DNA and in nuclear localization signal presence, resulting in members with and without DNA-binding properties. Only a few isoforms contain the requisite three or more N-terminal zinc motifs that confer high affinity binding to a specific core DNA sequence element in the promoters of target genes. The non-DNA-binding isoforms are largely found in the cytoplasm, and are thought to function as dominant-negative factors. Overexpression of some dominant-negative isoforms have been associated with B-cell malignancies, such as acute lymphoblastic leukemia (ALL). [provided by RefSeq, May 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IKZF1	NM_006060.6	c.*1656T>C		3_prime_UTR_variant	8/8	ENST00000331340.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IKZF1	ENST00000331340.8	c.*1656T>C		3_prime_UTR_variant	8/8	1	NM_006060.6	A1

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37329 AN: 152076 Hom.: 4805 Cov.: 33

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.253

GnomAD4 exome AF: 0.233 AC: 18195 AN: 78120 Hom.: 2320 Cov.: 0 AF XY: 0.232 AC XY: 8365 AN XY: 36006

Gnomad4 AFR exome AF: 0.206

Gnomad4 AMR exome AF: 0.234

Gnomad4 ASJ exome AF: 0.222

Gnomad4 EAS exome AF: 0.0883

Gnomad4 SAS exome AF: 0.275

Gnomad4 FIN exome AF: 0.339

Gnomad4 NFE exome AF: 0.268

Gnomad4 OTH exome AF: 0.237

GnomAD4 genome AF: 0.245 AC: 37356 AN: 152194 Hom.: 4810 Cov.: 33 AF XY: 0.249 AC XY: 18499 AN XY: 74408

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.328

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.249

Alfa AF: 0.262 Hom.: 10988

Bravo AF: 0.238

Asia WGS AF: 0.173 AC: 604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	4.1
Dann	Benign	0.64
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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

Other links and lift over

dbSNP: rs11980379; hg19: chr7-50469981;