chr9-7580951-A-G

Variant names:

• chr9-7580951-A-G
• rs2381645

Variant summary

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

The variant allele was found at a frequency of 0.612 in 152,014 control chromosomes in the GnomAD database, including 28,670 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 0.61 (28670 hom., cov: 32)
• Consequence: PPIAP33 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.18
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPIAP33		n.7580951A>G		intragenic_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.612 AC: 93002 AN: 151896 Hom.: 28641 Cov.: 32

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.612 AC: 93085 AN: 152014 Hom.: 28670 Cov.: 32 AF XY: 0.616 AC XY: 45742 AN XY: 74278

African (AFR) AF: 0.647 AC: 26831 AN: 41480

American (AMR) AF: 0.626 AC: 9552 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1849 AN: 3470

East Asian (EAS) AF: 0.792 AC: 4075 AN: 5146

South Asian (SAS) AF: 0.680 AC: 3278 AN: 4822

European-Finnish (FIN) AF: 0.620 AC: 6549 AN: 10560

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.575 AC: 39047 AN: 67964

Other (OTH) AF: 0.595 AC: 1254 AN: 2108

Alfa AF: 0.580 Hom.: 31349

Bravo AF: 0.615

Asia WGS AF: 0.730 AC: 2539 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	0.27
DANN	Benign	0.28
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs2381645; hg19: chr9-7580951;