10-79350551-C-T

Variant names:

• chr10-79350551-C-T
• rs1316313
• NM_005729.4:c.315+798C>T

Variant summary

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

The NM_005729.4(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 NM_005729.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.479
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005729.4. 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
	PPIF	NM_005729.4	MANE Select	c.315+798C>T		intron	N/A	NP_005720.1	P30405-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPIF	ENST00000225174.8	TSL:1 MANE Select	c.315+798C>T		intron	N/A	ENSP00000225174.3	P30405-1
	PPIF	ENST00000871351.1		c.315+798C>T		intron	N/A	ENSP00000541410.1
	PPIF	ENST00000955651.1		c.315+798C>T		intron	N/A	ENSP00000625710.1

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

African (AFR) AF: 0.181 AC: 7502 AN: 41516

American (AMR) AF: 0.401 AC: 6136 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1164 AN: 3472

East Asian (EAS) AF: 0.646 AC: 3323 AN: 5140

South Asian (SAS) AF: 0.374 AC: 1803 AN: 4826

European-Finnish (FIN) AF: 0.484 AC: 5111 AN: 10562

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.377 AC: 25613 AN: 67978

Other (OTH) AF: 0.371 AC: 783 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.1
DANN	Benign	0.87
PhyloP100		-0.48
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1316313; hg19: chr10-81110307;