rs7771722

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000357266.9(FKBP5):​c.-19-3378C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0428 in 152,282 control chromosomes in the GnomAD database, including 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 0.043 ( 213 hom., cov: 32)

Consequence

FKBP5
ENST00000357266.9 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.265
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 Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0901 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
FKBP5NM_004117.4 linkuse as main transcriptc.-19-3378C>T intron_variant ENST00000357266.9 NP_004108.1
FKBP5NM_001145775.3 linkuse as main transcriptc.-19-3378C>T intron_variant NP_001139247.1
FKBP5NM_001145776.2 linkuse as main transcriptc.-19-3378C>T intron_variant NP_001139248.1
FKBP5NM_001145777.2 linkuse as main transcriptc.-19-3378C>T intron_variant NP_001139249.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
FKBP5ENST00000357266.9 linkuse as main transcriptc.-19-3378C>T intron_variant 1 NM_004117.4 ENSP00000349811 P1Q13451-1
FKBP5ENST00000536438.5 linkuse as main transcriptc.-19-3378C>T intron_variant 1 ENSP00000444810 P1Q13451-1
FKBP5ENST00000539068.5 linkuse as main transcriptc.-19-3378C>T intron_variant 1 ENSP00000441205 P1Q13451-1
FKBP5ENST00000542713.1 linkuse as main transcriptc.-19-3378C>T intron_variant 2 ENSP00000442340 Q13451-2

Frequencies

GnomAD3 genomes
AF:
0.0428
AC:
6509
AN:
152164
Hom.:
213
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0927
Gnomad AMI
AF:
0.0482
Gnomad AMR
AF:
0.0299
Gnomad ASJ
AF:
0.0599
Gnomad EAS
AF:
0.000769
Gnomad SAS
AF:
0.00601
Gnomad FIN
AF:
0.0131
Gnomad MID
AF:
0.0633
Gnomad NFE
AF:
0.0247
Gnomad OTH
AF:
0.0415
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0428
AC:
6514
AN:
152282
Hom.:
213
Cov.:
32
AF XY:
0.0414
AC XY:
3082
AN XY:
74458
show subpopulations
Gnomad4 AFR
AF:
0.0926
Gnomad4 AMR
AF:
0.0299
Gnomad4 ASJ
AF:
0.0599
Gnomad4 EAS
AF:
0.000771
Gnomad4 SAS
AF:
0.00601
Gnomad4 FIN
AF:
0.0131
Gnomad4 NFE
AF:
0.0247
Gnomad4 OTH
AF:
0.0411
Alfa
AF:
0.0322
Hom.:
15
Bravo
AF:
0.0462
Asia WGS
AF:
0.00924
AC:
32
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.35
DANN
Benign
0.62

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs7771722; hg19: chr6-35613998; API