chr9-7565921-T-C

Variant names:

• chr9-7565921-T-C
• rs17543080

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 0.21 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
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.289 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: 0.211 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

African (AFR) AF: 0.0529 AC: 2196 AN: 41524

American (AMR) AF: 0.234 AC: 3564 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1015 AN: 3464

East Asian (EAS) AF: 0.0906 AC: 469 AN: 5174

South Asian (SAS) AF: 0.147 AC: 707 AN: 4816

European-Finnish (FIN) AF: 0.309 AC: 3268 AN: 10576

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19869 AN: 67924

Other (OTH) AF: 0.225 AC: 474 AN: 2110

Alfa AF: 0.233 Hom.: 2939

Bravo AF: 0.200

Asia WGS AF: 0.126 AC: 441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.8
DANN	Benign	0.44
PhyloP100		0.050

Splicing

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

Other links and lift over

dbSNP: rs17543080; hg19: chr9-7565921;