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GeneBe

rs1360780

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_004117.4(FKBP5):c.106-2636A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: not found (cov: 32)

Consequence

FKBP5
NM_004117.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0870
Variant links:
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 Likely_benign. Variant got -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FKBP5NM_004117.4 linkuse as main transcriptc.106-2636A>T intron_variant ENST00000357266.9
FKBP5NM_001145775.3 linkuse as main transcriptc.106-2636A>T intron_variant
FKBP5NM_001145776.2 linkuse as main transcriptc.106-2636A>T intron_variant
FKBP5NM_001145777.2 linkuse as main transcriptc.106-2636A>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FKBP5ENST00000357266.9 linkuse as main transcriptc.106-2636A>T intron_variant 1 NM_004117.4 P1Q13451-1
FKBP5ENST00000536438.5 linkuse as main transcriptc.106-2636A>T intron_variant 1 P1Q13451-1
FKBP5ENST00000539068.5 linkuse as main transcriptc.106-2636A>T intron_variant 1 P1Q13451-1
FKBP5ENST00000542713.1 linkuse as main transcriptc.106-2636A>T intron_variant 2 Q13451-2

Frequencies

GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
Cadd
Benign
4.6
Dann
Benign
0.71

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1360780; hg19: chr6-35607571; API