rs2092427
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004117.4(FKBP5):c.-19-11587C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0884 in 152,102 control chromosomes in the GnomAD database, including 1,213 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.088 ( 1213 hom., cov: 32)
Consequence
FKBP5
NM_004117.4 intron
NM_004117.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.147
Genes affected
FKBP5 (HGNC:3721): (FKBP prolyl isomerase 5) The protein encoded by this gene is a member of the immunophilin protein family, which play a role in immunoregulation and basic cellular processes involving protein folding and trafficking. This encoded protein is a cis-trans prolyl isomerase that binds to the immunosuppressants FK506 and rapamycin. It is thought to mediate calcineurin inhibition. It also interacts functionally with mature hetero-oligomeric progesterone receptor complexes along with the 90 kDa heat shock protein and P23 protein. This gene has been found to have multiple polyadenylation sites. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Mar 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FKBP5 | NM_004117.4 | c.-19-11587C>T | intron_variant | ENST00000357266.9 | |||
FKBP5 | NM_001145775.3 | c.-19-11587C>T | intron_variant | ||||
FKBP5 | NM_001145776.2 | c.-19-11587C>T | intron_variant | ||||
FKBP5 | NM_001145777.2 | c.-19-11587C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FKBP5 | ENST00000357266.9 | c.-19-11587C>T | intron_variant | 1 | NM_004117.4 | P1 | |||
FKBP5 | ENST00000536438.5 | c.-19-11587C>T | intron_variant | 1 | P1 | ||||
FKBP5 | ENST00000539068.5 | c.-19-11587C>T | intron_variant | 1 | P1 | ||||
FKBP5 | ENST00000542713.1 | c.-19-11587C>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0881 AC: 13387AN: 151984Hom.: 1199 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0884 AC: 13440AN: 152102Hom.: 1213 Cov.: 32 AF XY: 0.0870 AC XY: 6469AN XY: 74364
GnomAD4 genome
?
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13440
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152102
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32
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6469
AN XY:
74364
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140
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at