chr7-50319094-A-C

Variant names:

• chr7-50319094-A-C
• rs1480100906
• NM_006060.6:c.33A>C

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2 PP2 BP4_Moderate

The NM_006060.6(IKZF1):​c.33A>C​(p.Gln11His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000131 in 152,168 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.000013 (0 hom., cov: 32)
• Consequence: IKZF1 NM_006060.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.758

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 Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant in the IKZF1 gene, where missense mutations are typically associated with disease (based on misZ statistic). The gene has 11 curated pathogenic missense variants (we use a threshold of 10). The gene has 3 curated benign missense variants. Gene score misZ: 3.3753 (above the threshold of 3.09). Trascript score misZ: 3.423 (above the threshold of 3.09). GenCC associations: The gene is linked to autoimmune disease, pancytopenia due to IKZF1 mutations.
• BP4: Computational evidence support a benign effect (MetaRNN=0.19629833).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IKZF1	NM_006060.6	c.33A>C	p.Gln11His	missense_variant	Exon 2 of 8	ENST00000331340.8	NP_006051.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IKZF1	ENST00000331340.8	c.33A>C	p.Gln11His	missense_variant	Exon 2 of 8	1	NM_006060.6	ENSP00000331614.3

Frequencies

GnomAD3 genomes AF: 0.0000131 AC: 2 AN: 152168 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000483

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 29

GnomAD4 genome AF: 0.0000131 AC: 2 AN: 152168 Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1 AN XY: 74334

Gnomad4 AFR AF: 0.0000483

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000329 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.15
BayesDel_addAF	Benign	-0.14	T
BayesDel_noAF	Benign	-0.43
CADD	Benign	19
DANN	Uncertain	0.99
DEOGEN2	Benign	0.38	.;.;T;.;T;T;T;.;.;.;.;.;T;T;.;.;.
Eigen	Benign	0.0056
Eigen_PC	Benign	0.043
FATHMM_MKL	Uncertain	0.82	D
LIST_S2	Uncertain	0.92	D;D;.;.;D;D;D;.;D;D;D;T;T;T;D;.;D
M_CAP	Benign	0.0046	T
MetaRNN	Benign	0.20	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-1.1	T
PrimateAI	Benign	0.37	T
PROVEAN	Benign	-0.85	.;.;.;.;N;D;.;N;N;N;N;N;N;.;N;N;.
REVEL	Benign	0.11
Sift	Uncertain	0.0050	.;.;.;.;D;D;.;D;D;D;D;D;D;.;D;D;.
Sift4G	Benign	0.13	.;.;.;.;T;D;D;T;T;D;T;T;T;D;T;D;.
Polyphen		0.41, 1.0, 0.77, 0.73	.;.;B;.;B;D;.;P;.;P;.;.;.;.;P;P;.
Vest4		0.13, 0.35, 0.15, 0.13, 0.11, 0.18, 0.17, 0.18, 0.14, 0.19, 0.18
MutPred		0.18		Loss of methylation at K15 (P = 0.2088);Loss of methylation at K15 (P = 0.2088);Loss of methylation at K15 (P = 0.2088);Loss of methylation at K15 (P = 0.2088);Loss of methylation at K15 (P = 0.2088);Loss of methylation at K15 (P = 0.2088);Loss of methylation at K15 (P = 0.2088);Loss of methylation at K15 (P = 0.2088);Loss of methylation at K15 (P = 0.2088);Loss of methylation at K15 (P = 0.2088);Loss of methylation at K15 (P = 0.2088);Loss of methylation at K15 (P = 0.2088);Loss of methylation at K15 (P = 0.2088);Loss of methylation at K15 (P = 0.2088);Loss of methylation at K15 (P = 0.2088);Loss of methylation at K15 (P = 0.2088);Loss of methylation at K15 (P = 0.2088);
MVP		0.48
MPC		0.89
ClinPred		0.64	D
GERP RS		2.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.13
gMVP		0.23

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: rs1480100906; hg19: chr7-50358690; COSMIC: COSV105893518;