1-23019623-C-CGCG
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_001009999.3(KDM1A):c.39_41dupGGC(p.Ala14dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000395 in 1,418,088 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001009999.3 disruptive_inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 151712Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000395 AC: 50AN: 1266376Hom.: 0 Cov.: 31 AF XY: 0.0000369 AC XY: 23AN XY: 623036
GnomAD4 genome AF: 0.0000395 AC: 6AN: 151712Hom.: 0 Cov.: 32 AF XY: 0.0000405 AC XY: 3AN XY: 74086
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
KDM1A: BP3 -
This variant, c.39_41dup, results in the insertion of 1 amino acid(s) of the KDM1A protein (p.Ala18dup), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (no rsID available, gnomAD 0.002%). This variant has not been reported in the literature in individuals affected with KDM1A-related conditions. 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