rs10976413

Positions:

• chr9-7573504-T-C
• chr9-7573504-T-G

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 0.213 in 152,010 control chromosomes in the GnomAD database, including 4,389 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 0.21 (4389 hom., cov: 32)
• Consequence: PPIAP33 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.980

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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PPIAP33		n.7573504T>C		intragenic_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32362 AN: 151892 Hom.: 4389 Cov.: 32

Gnomad AFR AF: 0.0544

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.0642

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.213 AC: 32358 AN: 152010 Hom.: 4389 Cov.: 32 AF XY: 0.212 AC XY: 15737 AN XY: 74288

Gnomad4 AFR AF: 0.0543

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.292

Gnomad4 EAS AF: 0.0648

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.231

Alfa AF: 0.167 Hom.: 430

Bravo AF: 0.203

Asia WGS AF: 0.116 AC: 404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.9
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10976413; hg19: chr9-7573504;