1-39722441-C-T

Variant names:

• chr1-39722441-C-T
• rs704784
• ENST00000470018.5:c.-325-13027C>T

Variant summary

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

The ENST00000470018.5(PPIE):​c.-325-13027C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 152,064 control chromosomes in the GnomAD database, including 25,668 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 0.58 (25668 hom., cov: 32)
• Consequence: PPIE ENST00000470018.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160
• Publications: 5 publications found

Genes affected

PPIE (HGNC:9258): (peptidylprolyl isomerase E) 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 contains a highly conserved cyclophilin (CYP) domain as well as an RNA-binding domain. It was shown to possess PPIase and protein folding activities, and it also exhibits RNA-binding activity. Alternative splicing results in multiple transcript variants. A related pseudogene, which is also located on chromosome 1, has been identified. [provided by RefSeq, Aug 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000470018.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPIE	ENST00000470018.5	TSL:5	c.-325-13027C>T		intron	N/A	ENSP00000436689.1	E9PIB0

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87653 AN: 151946 Hom.: 25633 Cov.: 32

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.799

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.577 AC: 87746 AN: 152064 Hom.: 25668 Cov.: 32 AF XY: 0.578 AC XY: 42985 AN XY: 74316

African (AFR) AF: 0.616 AC: 25572 AN: 41480

American (AMR) AF: 0.542 AC: 8292 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 2138 AN: 3470

East Asian (EAS) AF: 0.799 AC: 4141 AN: 5180

South Asian (SAS) AF: 0.663 AC: 3192 AN: 4818

European-Finnish (FIN) AF: 0.557 AC: 5881 AN: 10550

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.540 AC: 36718 AN: 67958

Other (OTH) AF: 0.551 AC: 1163 AN: 2112

Alfa AF: 0.553 Hom.: 63830

Bravo AF: 0.575

Asia WGS AF: 0.698 AC: 2426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.0
DANN	Benign	0.46
PhyloP100		-0.016

Splicing

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

Other links and lift over

dbSNP: rs704784; hg19: chr1-40188113;