rs4459609

Variant names:

• chr17-63471587-C-A
• rs4459609
• ENST00000606284.1:n.-17C>A

Your query was ambiguous. Multiple possible variants found:

• chr17-63471587-C-A
• chr17-63471587-C-T

Variant summary

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

The ENST00000606284.1(PPIAP55):​n.-17C>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
• Publications: 44 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPIAP55	ENST00000606284.1	n.-17C>A		upstream_gene_variant		6

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

African (AFR) AF: 0.645 AC: 10854 AN: 16822

American (AMR) AF: 0.706 AC: 27484 AN: 38908

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 9433 AN: 17900

East Asian (EAS) AF: 0.633 AC: 22330 AN: 35296

South Asian (SAS) AF: 0.619 AC: 38709 AN: 62558

European-Finnish (FIN) AF: 0.620 AC: 25872 AN: 41702

Middle Eastern (MID) AF: 0.531 AC: 2072 AN: 3904

European-Non Finnish (NFE) AF: 0.612 AC: 217789 AN: 355840

Other (OTH) AF: 0.610 AC: 19099 AN: 31302

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

African (AFR) AF: 0.650 AC: 26923 AN: 41392

American (AMR) AF: 0.667 AC: 10163 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1871 AN: 3468

East Asian (EAS) AF: 0.642 AC: 3312 AN: 5158

South Asian (SAS) AF: 0.622 AC: 2996 AN: 4820

European-Finnish (FIN) AF: 0.616 AC: 6481 AN: 10528

Middle Eastern (MID) AF: 0.500 AC: 146 AN: 292

European-Non Finnish (NFE) AF: 0.616 AC: 41854 AN: 67960

Other (OTH) AF: 0.608 AC: 1283 AN: 2110

Alfa AF: 0.619 Hom.: 80166

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
PhyloP100		-0.0070

Splicing

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

Other links and lift over

dbSNP: rs4459609; hg19: chr17-61548948;