4-48500154-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015030.2(FRYL):c.8659G>A(p.Glu2887Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000212 in 1,606,538 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015030.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000206 AC: 5AN: 242310Hom.: 0 AF XY: 0.00000760 AC XY: 1AN XY: 131542
GnomAD4 exome AF: 0.0000199 AC: 29AN: 1454264Hom.: 0 Cov.: 30 AF XY: 0.0000152 AC XY: 11AN XY: 723302
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152274Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74464
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.8659G>A (p.E2887K) alteration is located in exon 63 (coding exon 60) of the FRYL gene. This alteration results from a G to A substitution at nucleotide position 8659, causing the glutamic acid (E) at amino acid position 2887 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at