rs9462099

Variant names:

• chr6-35613027-T-C
• rs9462099
• NM_004117.4:c.508+6069A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_004117.4(FKBP5):​c.508+6069A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00909 in 152,214 control chromosomes in the GnomAD database, including 21 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 0.0091 (21 hom., cov: 32)
• Consequence: FKBP5 NM_004117.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.561

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00909 (1383/152214) while in subpopulation AFR AF= 0.0302 (1253/41536). AF 95% confidence interval is 0.0288. There are 21 homozygotes in gnomad4. There are 658 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 21 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FKBP5	NM_004117.4	c.508+6069A>G		intron_variant	Intron 5 of 10	ENST00000357266.9	NP_004108.1
FKBP5	NM_001145775.3	c.508+6069A>G		intron_variant	Intron 6 of 11		NP_001139247.1
FKBP5	NM_001145776.2	c.508+6069A>G		intron_variant	Intron 5 of 10		NP_001139248.1
FKBP5	NM_001145777.2	c.508+6069A>G		intron_variant	Intron 5 of 6		NP_001139249.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FKBP5	ENST00000357266.9	c.508+6069A>G		intron_variant	Intron 5 of 10	1	NM_004117.4	ENSP00000349811.3
FKBP5	ENST00000536438.5	c.508+6069A>G		intron_variant	Intron 6 of 11	1		ENSP00000444810.1
FKBP5	ENST00000539068.5	c.508+6069A>G		intron_variant	Intron 5 of 10	1		ENSP00000441205.1
FKBP5	ENST00000542713.1	c.508+6069A>G		intron_variant	Intron 5 of 6	2		ENSP00000442340.1

Frequencies

GnomAD3 genomes AF: 0.00907 AC: 1380 AN: 152096 Hom.: 21 Cov.: 32

Gnomad AFR AF: 0.0302

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00583

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000162

Gnomad OTH AF: 0.00861

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

GnomAD4 genome AF: 0.00909 AC: 1383 AN: 152214 Hom.: 21 Cov.: 32 AF XY: 0.00884 AC XY: 658 AN XY: 74430

Gnomad4 AFR AF: 0.0302

Gnomad4 AMR AF: 0.00582

Gnomad4 ASJ AF: 0.00317

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000162

Gnomad4 OTH AF: 0.00852

Alfa AF: 0.00818 Hom.: 1

Bravo AF: 0.0100

Asia WGS AF: 0.00202 AC: 7 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.2
DANN	Benign	0.64

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: rs9462099; hg19: chr6-35580804;