7-50327649-C-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP2BS2
The NM_006060.6(IKZF1):c.52C>A(p.Pro18Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000822 in 1,460,098 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006060.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000822 AC: 12AN: 1460098Hom.: 0 Cov.: 30 AF XY: 0.00000551 AC XY: 4AN XY: 726208
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change replaces proline, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 18 of the IKZF1 protein (p.Pro18Thr). This variant is present in population databases (rs754640737, gnomAD 0.006%). This missense change has been observed in individual(s) with Acute Lymphoblastic Leukemia (PMID: 29681510). ClinVar contains an entry for this variant (Variation ID: 1972179). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. Experimental studies have shown that this missense change does not substantially affect IKZF1 function (PMID: 29681510). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at