chr10-79350551-C-T

Position:

• chr10-79350551-C-T

Variant summary

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

The ENST00000225174.8(PPIF):​c.315+798C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 152,104 control chromosomes in the GnomAD database, including 9,974 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 0.34 (9974 hom., cov: 33)
• Consequence: PPIF ENST00000225174.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.479

Genes affected

PPIF (HGNC:9259): (peptidylprolyl isomerase F) The protein encoded by this gene is a member of the peptidyl-prolyl cis-trans isomerase (PPIase) family. PPIases catalyze the cis-trans isomerization of proline imidic peptide bonds in oligopeptides and accelerate the folding of proteins. This protein is part of the mitochondrial permeability transition pore in the inner mitochondrial membrane. Activation of this pore is thought to be involved in the induction of apoptotic and necrotic cell death. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PPIF	NM_005729.4	c.315+798C>T		intron_variant		ENST00000225174.8	NP_005720.1
PPIF	XM_005269379.3	c.315+798C>T		intron_variant			XP_005269436.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPIF	ENST00000225174.8	c.315+798C>T		intron_variant		1	NM_005729.4	ENSP00000225174	P1
PPIF	ENST00000448165.1	c.206+798C>T		intron_variant		2		ENSP00000396388
PPIF	ENST00000472580.6	c.315+798C>T		intron_variant, NMD_transcript_variant		5		ENSP00000473548
PPIF	ENST00000498681.5	n.395+798C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51907 AN: 151986 Hom.: 9969 Cov.: 33

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.341 AC: 51920 AN: 152104 Hom.: 9974 Cov.: 33 AF XY: 0.350 AC XY: 25997 AN XY: 74330

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.401

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.646

Gnomad4 SAS AF: 0.374

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.377

Gnomad4 OTH AF: 0.371

Alfa AF: 0.237 Hom.: 688

Bravo AF: 0.329

Asia WGS AF: 0.481 AC: 1674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.1
DANN	Benign	0.87
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs1316313; hg19: chr10-81110307;