9-113169312-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015258.2(FKBP15):c.3397G>A(p.Gly1133Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000297 in 1,613,904 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015258.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FKBP15 | NM_015258.2 | c.3397G>A | p.Gly1133Ser | missense_variant | Exon 26 of 28 | ENST00000238256.8 | NP_056073.1 | |
FKBP15 | XM_006717018.3 | c.3367G>A | p.Gly1123Ser | missense_variant | Exon 26 of 28 | XP_006717081.1 | ||
FKBP15 | XM_006717019.2 | c.3193G>A | p.Gly1065Ser | missense_variant | Exon 25 of 27 | XP_006717082.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152196Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000361 AC: 9AN: 249244Hom.: 0 AF XY: 0.0000444 AC XY: 6AN XY: 135206
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1461708Hom.: 0 Cov.: 30 AF XY: 0.0000275 AC XY: 20AN XY: 727136
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152196Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3397G>A (p.G1133S) alteration is located in exon 26 (coding exon 26) of the FKBP15 gene. This alteration results from a G to A substitution at nucleotide position 3397, causing the glycine (G) at amino acid position 1133 to be replaced by a serine (S). 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