rs4713902

chr6-35646249-T-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 1P and 9B. PP5 BP4 BA1

The NM_004117.4(FKBP5):c.-19-3406A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 152,214 control chromosomes in the GnomAD database, including 4,322 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely risk allele (no stars).

• Frequency: Genomes: 𝑓 0.22 (4322 hom., cov: 33)
• Consequence: FKBP5 NM_004117.4 intron
• Clinical Significance: Likely risk allele no assertion criteria provided P:1
• Conservation: PhyloP100: -0.332

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]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• PP5: Variant 6-35646249-T-C is Pathogenic according to our data. Variant chr6-35646249-T-C is described in ClinVar as [Likely_risk_allele]. Clinvar id is 1702947.Status of the report is no_assertion_criteria_provided, 0 stars. We mark this variant Likely_pathogenic, oryginal submission is: [Likely_risk_allele].
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).. Strength limited to SUPPORTING due to the PP5.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FKBP5	NM_004117.4	c.-19-3406A>G		intron_variant		ENST00000357266.9
FKBP5	NM_001145775.3	c.-19-3406A>G		intron_variant
FKBP5	NM_001145776.2	c.-19-3406A>G		intron_variant
FKBP5	NM_001145777.2	c.-19-3406A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FKBP5	ENST00000357266.9	c.-19-3406A>G		intron_variant		1	NM_004117.4	P1
FKBP5	ENST00000536438.5	c.-19-3406A>G		intron_variant		1		P1
FKBP5	ENST00000539068.5	c.-19-3406A>G		intron_variant		1		P1
FKBP5	ENST00000542713.1	c.-19-3406A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33133 AN: 152096 Hom.: 4314 Cov.: 33

Gnomad AFR AF: 0.0778

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.257

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.218 AC: 33150 AN: 152214 Hom.: 4322 Cov.: 33 AF XY: 0.217 AC XY: 16113 AN XY: 74416

Gnomad4 AFR AF: 0.0777

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.234

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.257

Alfa AF: 0.259 Hom.: 4163

Bravo AF: 0.218

Asia WGS AF: 0.244 AC: 847 AN: 3478

ClinVar

Significance: Likely risk allele

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Susceptibility to severe depressive disorder Pathogenic:1

Likely risk allele, no assertion criteria provided

case-control

Beijing Key Laboratory of Neuropsychopharmacology, State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology

Jul 01, 2022

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.98
Dann	Benign	0.69

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

Other links and lift over

dbSNP: rs4713902; hg19: chr6-35614026;