17-41812768-G-T

Variant names:

• chr17-41812768-G-T
• rs114527140
• ENST00000585664.5:c.-23+29G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000585664.5(FKBP10):​c.-23+29G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: FKBP10 ENST00000585664.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.411
• Publications: 0 publications found

Genes affected

FKBP10 (HGNC:18169): (FKBP prolyl isomerase 10) The protein encoded by this gene belongs to the FKBP-type peptidyl-prolyl cis/trans isomerase (PPIase) family. This protein localizes to the endoplasmic reticulum and acts as a molecular chaperone. Alternatively spliced variants encoding different isoforms have been reported, but their biological validity has not been determined.[provided by RefSeq, Nov 2009]

P3H4 (HGNC:16946): (prolyl 3-hydroxylase family member 4 (inactive)) This nucleolar protein was first characterized because it was an autoantigen in cases on interstitial cystitis. The protein, with a predicted molecular weight of 50 kDa, appears to be localized in the particulate compartment of the interphase nucleolus, with a distribution distinct from that of nucleolar protein B23. During mitosis it is associated with chromosomes. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FKBP10	NM_021939.4	c.-267G>T		upstream_gene_variant		ENST00000321562.9	NP_068758.3
FKBP10	XM_011525099.4	c.-267G>T		upstream_gene_variant			XP_011523401.1
FKBP10	XM_011525100.3	c.-394G>T		upstream_gene_variant			XP_011523402.1
FKBP10	XM_047436515.1	c.-394G>T		upstream_gene_variant			XP_047292471.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FKBP10	ENST00000321562.9	c.-267G>T		upstream_gene_variant		1	NM_021939.4	ENSP00000317232.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 396402 Hom.: 0 Cov.: 4 AF XY: 0.00 AC XY: 0 AN XY: 210074

African (AFR) AF: 0.00 AC: 0 AN: 11164

American (AMR) AF: 0.00 AC: 0 AN: 17052

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12098

East Asian (EAS) AF: 0.00 AC: 0 AN: 25632

South Asian (SAS) AF: 0.00 AC: 0 AN: 45052

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 24170

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1734

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 236712

Other (OTH) AF: 0.00 AC: 0 AN: 22788

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	9.8
DANN	Benign	0.80
PhyloP100		-0.41
PromoterAI		-0.069	Neutral

Splicing

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

Other links and lift over

dbSNP: rs114527140; hg19: chr17-39969020;