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GeneBe

rs3800373

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_004117.4(FKBP5):c.*1136G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.68 in 152,464 control chromosomes in the GnomAD database, including 35,585 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.68 ( 35446 hom., cov: 33)
Exomes 𝑓: 0.81 ( 139 hom. )

Consequence

FKBP5
NM_004117.4 3_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.222
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 -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 6-35574699-C-A is Benign according to our data. Variant chr6-35574699-C-A is described in ClinVar as [Benign]. Clinvar id is 1279819.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FKBP5NM_004117.4 linkuse as main transcriptc.*1136G>T 3_prime_UTR_variant 11/11 ENST00000357266.9
LOC101929309XR_242006.4 linkuse as main transcriptn.182-18331C>A intron_variant, non_coding_transcript_variant
FKBP5NM_001145775.3 linkuse as main transcriptc.*1136G>T 3_prime_UTR_variant 12/12
FKBP5NM_001145776.2 linkuse as main transcriptc.*1136G>T 3_prime_UTR_variant 11/11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FKBP5ENST00000357266.9 linkuse as main transcriptc.*1136G>T 3_prime_UTR_variant 11/111 NM_004117.4 P1Q13451-1
FKBP5ENST00000536438.5 linkuse as main transcriptc.*1136G>T 3_prime_UTR_variant 12/121 P1Q13451-1
FKBP5ENST00000539068.5 linkuse as main transcriptc.*1136G>T 3_prime_UTR_variant 11/111 P1Q13451-1

Frequencies

GnomAD3 genomes
AF:
0.679
AC:
103224
AN:
151932
Hom.:
35419
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.572
Gnomad AMI
AF:
0.844
Gnomad AMR
AF:
0.675
Gnomad ASJ
AF:
0.714
Gnomad EAS
AF:
0.742
Gnomad SAS
AF:
0.663
Gnomad FIN
AF:
0.813
Gnomad MID
AF:
0.656
Gnomad NFE
AF:
0.718
Gnomad OTH
AF:
0.661
GnomAD4 exome
AF:
0.813
AC:
335
AN:
412
Hom.:
139
Cov.:
0
AF XY:
0.836
AC XY:
209
AN XY:
250
show subpopulations
Gnomad4 FIN exome
AF:
0.814
Gnomad4 OTH exome
AF:
0.750
GnomAD4 genome
AF:
0.679
AC:
103294
AN:
152052
Hom.:
35446
Cov.:
33
AF XY:
0.684
AC XY:
50846
AN XY:
74330
show subpopulations
Gnomad4 AFR
AF:
0.572
Gnomad4 AMR
AF:
0.675
Gnomad4 ASJ
AF:
0.714
Gnomad4 EAS
AF:
0.742
Gnomad4 SAS
AF:
0.664
Gnomad4 FIN
AF:
0.813
Gnomad4 NFE
AF:
0.718
Gnomad4 OTH
AF:
0.656
Alfa
AF:
0.711
Hom.:
66774
Bravo
AF:
0.665
Asia WGS
AF:
0.688
AC:
2389
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJan 18, 2019This variant is associated with the following publications: (PMID: 30150364, 31071710) -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
Cadd
Benign
1.4
Dann
Benign
0.50

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: rs3800373; hg19: chr6-35542476; COSMIC: COSV61881577; API