rs10759243

Variant names:

• chr9-107543834-C-A
• rs10759243
• ENST00000422463.1:n.-218G>T

Your query was ambiguous. Multiple possible variants found:

• chr9-107543834-C-A
• chr9-107543834-C-T

Variant summary

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

The ENST00000422463.1(PPIAP88):​n.-218G>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 151,966 control chromosomes in the GnomAD database, including 13,929 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 0.40 (13929 hom., cov: 33)
• Consequence: PPIAP88 ENST00000422463.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.166

Genes affected

PPIAP88 (HGNC:53712): (peptidylprolyl isomerase A pseudogene 88)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.605 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
PPIAP88	ENST00000422463.1	n.-218G>T		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61274 AN: 151848 Hom.: 13889 Cov.: 33

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.404 AC: 61370 AN: 151966 Hom.: 13929 Cov.: 33 AF XY: 0.407 AC XY: 30223 AN XY: 74270

Gnomad4 AFR AF: 0.611

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.393

Gnomad4 FIN AF: 0.325

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.404

Alfa AF: 0.288 Hom.: 2606

Bravo AF: 0.420

Asia WGS AF: 0.454 AC: 1582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.88
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: rs10759243; hg19: chr9-110306115; COSMIC: COSV69656636;