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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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 v4.9

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;