rs4459609

chr17-63471587-C-A

Variant summary

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

The 17-63471587-C-A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 756,116 control chromosomes in the GnomAD database, including 146,417 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 0.63 (30043 hom., cov: 31)
  • Exomes 𝑓: 0.62 (116374 hom.)
• Consequence: PPIAP55 ENST00000606284.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700

Genes affected

PPIAP55 (HGNC:53679): (peptidylprolyl isomerase A pseudogene 55)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPIAP55	ENST00000606284.1			upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.629 AC: 95465 AN: 151766 Hom.: 30013 Cov.: 31

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.642

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.613

GnomAD4 exome AF: 0.618 AC: 373642 AN: 604232 Hom.: 116374 Cov.: 6 AF XY: 0.615 AC XY: 200930 AN XY: 326546

Gnomad4 AFR exome AF: 0.645

Gnomad4 AMR exome AF: 0.706

Gnomad4 ASJ exome AF: 0.527

Gnomad4 EAS exome AF: 0.633

Gnomad4 SAS exome AF: 0.619

Gnomad4 FIN exome AF: 0.620

Gnomad4 NFE exome AF: 0.612

Gnomad4 OTH exome AF: 0.610

GnomAD4 genome AF: 0.629 AC: 95551 AN: 151884 Hom.: 30043 Cov.: 31 AF XY: 0.629 AC XY: 46720 AN XY: 74224

Gnomad4 AFR AF: 0.650

Gnomad4 AMR AF: 0.667

Gnomad4 ASJ AF: 0.540

Gnomad4 EAS AF: 0.642

Gnomad4 SAS AF: 0.622

Gnomad4 FIN AF: 0.616

Gnomad4 NFE AF: 0.616

Gnomad4 OTH AF: 0.608

Alfa AF: 0.613 Hom.: 45659

Bravo AF: 0.632

Asia WGS AF: 0.644 AC: 2238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.61
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4459609; hg19: chr17-61548948;