rs17339199

chr7-73357128-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003602.5(FKBP6):c.*3-1053T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.951 in 152,212 control chromosomes in the GnomAD database, including 68,982 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 0.95 (68982 hom., cov: 30)
• Consequence: FKBP6 NM_003602.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

Genes affected

FKBP6 (HGNC:3722): (FKBP prolyl isomerase family member 6 (inactive)) The protein encoded by this gene is a cis-trans peptidyl-prolyl isomerase that may function in immunoregulation and basic cellular processes involving protein folding and trafficking. This gene is located in a chromosomal region that is deleted in Williams-Beuren syndrome. Defects in this gene may cause male infertility. There are multiple pseudogenes for this gene located nearby on chromosome 7. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.98 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FKBP6	NM_003602.5	c.*3-1053T>C		intron_variant		ENST00000252037.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FKBP6	ENST00000252037.5	c.*3-1053T>C		intron_variant		1	NM_003602.5	P4
FKBP6	ENST00000413573.6	c.*3-1053T>C		intron_variant		5
FKBP6	ENST00000431982.6	c.*3-1053T>C		intron_variant		2		A1
FKBP6	ENST00000445032.5	c.*1066-1053T>C		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.951 AC: 144707 AN: 152094 Hom.: 68926 Cov.: 30

Gnomad AFR AF: 0.988

Gnomad AMI AF: 0.916

Gnomad AMR AF: 0.885

Gnomad ASJ AF: 0.962

Gnomad EAS AF: 0.910

Gnomad SAS AF: 0.988

Gnomad FIN AF: 0.964

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.943

Gnomad OTH AF: 0.941

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

GnomAD4 genome AF: 0.951 AC: 144816 AN: 152212 Hom.: 68982 Cov.: 30 AF XY: 0.951 AC XY: 70767 AN XY: 74412

Gnomad4 AFR AF: 0.988

Gnomad4 AMR AF: 0.884

Gnomad4 ASJ AF: 0.962

Gnomad4 EAS AF: 0.911

Gnomad4 SAS AF: 0.988

Gnomad4 FIN AF: 0.964

Gnomad4 NFE AF: 0.943

Gnomad4 OTH AF: 0.942

Alfa AF: 0.938 Hom.: 46634

Bravo AF: 0.943

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17339199; hg19: chr7-72771137;