rs7763535

Variant names:

• chr6-35694329-C-A
• rs7763535
• ENST00000536438.5:c.-20+25999G>T

Your query was ambiguous. Multiple possible variants found:

• chr6-35694329-C-A
• chr6-35694329-C-G
• chr6-35694329-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001145775.3(FKBP5):​c.-20+25999G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.773 in 151,828 control chromosomes in the GnomAD database, including 45,865 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 0.77 (45865 hom., cov: 29)
• Consequence: FKBP5 NM_001145775.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.843
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001145775.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FKBP5	NM_001145775.3		c.-20+25999G>T		intron	N/A	NP_001139247.1	Q13451-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FKBP5	ENST00000536438.5	TSL:1	c.-20+25999G>T		intron	N/A	ENSP00000444810.1	Q13451-1
	FKBP5	ENST00000893094.1		c.-20+25999G>T		intron	N/A	ENSP00000563153.1
	FKBP5	ENST00000893095.1		c.-78-9844G>T		intron	N/A	ENSP00000563154.1

Frequencies

GnomAD3 genomes AF: 0.773 AC: 117250 AN: 151710 Hom.: 45805 Cov.: 29

Gnomad AFR AF: 0.897

Gnomad AMI AF: 0.747

Gnomad AMR AF: 0.733

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.736

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.758

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

GnomAD4 genome AF: 0.773 AC: 117368 AN: 151828 Hom.: 45865 Cov.: 29 AF XY: 0.774 AC XY: 57432 AN XY: 74172

African (AFR) AF: 0.897 AC: 37148 AN: 41410

American (AMR) AF: 0.734 AC: 11192 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.791 AC: 2746 AN: 3470

East Asian (EAS) AF: 0.777 AC: 4001 AN: 5150

South Asian (SAS) AF: 0.673 AC: 3237 AN: 4812

European-Finnish (FIN) AF: 0.782 AC: 8242 AN: 10542

Middle Eastern (MID) AF: 0.726 AC: 212 AN: 292

European-Non Finnish (NFE) AF: 0.712 AC: 48322 AN: 67880

Other (OTH) AF: 0.754 AC: 1587 AN: 2104

Alfa AF: 0.711 Hom.: 3280

Bravo AF: 0.777

Asia WGS AF: 0.722 AC: 2507 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.6
DANN	Benign	0.82
PhyloP100		-0.84
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs7763535; hg19: chr6-35662106;