10-75022147-GGAAGAAGAAGAA-GGAA
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_012330.4(KAT6B):c.3304_3312delGAAGAAGAA(p.Glu1102_Glu1104del) variant causes a conservative inframe deletion change. The variant allele was found at a frequency of 0.0000436 in 1,605,902 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_012330.4 conservative_inframe_deletion
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000333 AC: 5AN: 150036Hom.: 0 Cov.: 22
GnomAD3 exomes AF: 0.0000210 AC: 5AN: 238206Hom.: 0 AF XY: 0.0000231 AC XY: 3AN XY: 129600
GnomAD4 exome AF: 0.0000446 AC: 65AN: 1455866Hom.: 0 AF XY: 0.0000442 AC XY: 32AN XY: 724470
GnomAD4 genome AF: 0.0000333 AC: 5AN: 150036Hom.: 0 Cov.: 22 AF XY: 0.0000410 AC XY: 3AN XY: 73172
ClinVar
Submissions by phenotype
Genitopatellar syndrome Uncertain:1
This variant, c.3304_3312del, results in the deletion of 3 amino acid(s) of the KAT6B protein (p.Glu1102_Glu1104del), but otherwise preserves the integrity of the reading frame. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with KAT6B-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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