NM_032590.5:c.*163G>A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_032590.5(KDM2B):c.*163G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000797 in 1,613,820 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_032590.5 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000631 AC: 96AN: 152194Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00172 AC: 428AN: 249380Hom.: 2 AF XY: 0.00202 AC XY: 274AN XY: 135338
GnomAD4 exome AF: 0.000814 AC: 1190AN: 1461508Hom.: 15 Cov.: 31 AF XY: 0.00111 AC XY: 809AN XY: 727122
GnomAD4 genome AF: 0.000630 AC: 96AN: 152312Hom.: 0 Cov.: 32 AF XY: 0.000765 AC XY: 57AN XY: 74474
ClinVar
Submissions by phenotype
KDM2B-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at