11-64211102-GAGAAGA-GAGA
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP3BS1_Supporting
The NM_031471.6(FERMT3):c.456_458delGAA(p.Lys153del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.000155 in 1,571,054 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_031471.6 disruptive_inframe_deletion
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: 0.0000858 AC: 13AN: 151528Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000113 AC: 20AN: 176786Hom.: 0 AF XY: 0.000116 AC XY: 11AN XY: 94832
GnomAD4 exome AF: 0.000163 AC: 231AN: 1419526Hom.: 0 AF XY: 0.000155 AC XY: 109AN XY: 702474
GnomAD4 genome AF: 0.0000858 AC: 13AN: 151528Hom.: 0 Cov.: 32 AF XY: 0.000149 AC XY: 11AN XY: 73948
ClinVar
Submissions by phenotype
Leukocyte adhesion deficiency 3 Uncertain:1
This variant, c.456_458del, results in the deletion of 1 amino acid(s) of the FERMT3 protein (p.Lys153del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs759155629, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with FERMT3-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