chr12-121580866-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PVS1_StrongBS2
The NM_032590.5(KDM2B):c.46C>T(p.Arg16*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000366 in 1,613,642 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032590.5 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000658 AC: 10AN: 152014Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000802 AC: 2AN: 249334Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135278
GnomAD4 exome AF: 0.0000335 AC: 49AN: 1461628Hom.: 0 Cov.: 33 AF XY: 0.0000385 AC XY: 28AN XY: 727134
GnomAD4 genome AF: 0.0000658 AC: 10AN: 152014Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74240
ClinVar
Submissions by phenotype
not specified Uncertain:1
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Protein has effects on proliferation and DNA repair. Gene associated with acute myeloid leukemia, pancreatic cancer. Low level of KDM2B found in agressive brain tumors (according to a dissertation from 2008). However, exon 1 is poorly conserved, and there is a framshift variant in this exon in 0.4% of European chromosomes. There really isn't sufficient evidence available to conclude that KDM2B variants cause cancer in humans (no reports of specific variants, just expression studies in tumors and in vitro studies) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at