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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 0.679 in 151932 control chromosomes in the gnomAD Genomes database, including 35419 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.68 ( 35419 hom., cov: 33)

Consequence

FKBP5
NM_004117.4 3_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.222

Links

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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
?
GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.722 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
AF XY:
0.836
AC XY:
209
AN XY:
250
show subpopulations
Gnomad4 FIN exome
AF:
0.814
Gnomad4 OTH exome
AF:
0.750
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
3.0
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