rs2381640

Positions:

• chr9-7560779-C-T

Variant summary

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

The variant allele was found at a frequency of 0.299 in 152,022 control chromosomes in the GnomAD database, including 7,582 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 0.30 (7582 hom., cov: 32)
• Consequence: PPIAP33 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581

Genes affected

PPIAP33 (HGNC:49752): (peptidylprolyl isomerase A pseudogene 33)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PPIAP33		n.7560779C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45460 AN: 151902 Hom.: 7573 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.299 AC: 45492 AN: 152022 Hom.: 7582 Cov.: 32 AF XY: 0.307 AC XY: 22828 AN XY: 74294

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.658

Gnomad4 SAS AF: 0.502

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.299

Alfa AF: 0.289 Hom.: 3679

Bravo AF: 0.304

Asia WGS AF: 0.547 AC: 1899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.6
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2381640; hg19: chr9-7560779;