9-7573504-T-C

Variant names:

• chr9-7573504-T-C
• rs10976413

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 0.213 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
• 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.0543 AC: 2253 AN: 41488

American (AMR) AF: 0.236 AC: 3608 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.292 AC: 1011 AN: 3468

East Asian (EAS) AF: 0.0648 AC: 334 AN: 5156

South Asian (SAS) AF: 0.176 AC: 847 AN: 4822

European-Finnish (FIN) AF: 0.289 AC: 3061 AN: 10578

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20326 AN: 67924

Other (OTH) AF: 0.231 AC: 488 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.9
DANN	Benign	0.87
PhyloP100		0.98

Splicing

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

Other links and lift over

dbSNP: rs10976413; hg19: chr9-7573504;