9-7565921-T-C

Variant names:

• chr9-7565921-T-C
• rs17543080

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 0.21 in 152,050 control chromosomes in the GnomAD database, including 4,303 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 (4303 hom., cov: 32)
• Consequence: PPIAP33 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0500

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPIAP33		n.7565921T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.211 AC: 31987 AN: 151932 Hom.: 4301 Cov.: 32

Gnomad AFR AF: 0.0530

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.0897

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.210 AC: 31987 AN: 152050 Hom.: 4303 Cov.: 32 AF XY: 0.210 AC XY: 15620 AN XY: 74304

Gnomad4 AFR AF: 0.0529

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.0906

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.225

Alfa AF: 0.234 Hom.: 1583

Bravo AF: 0.200

Asia WGS AF: 0.126 AC: 441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.8
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17543080; hg19: chr9-7565921;