rs4400445

Variant names:

• chr9-7558261-C-T
• rs4400445

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 0.164 in 152,116 control chromosomes in the GnomAD database, including 2,162 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 0.16 (2162 hom., cov: 32)
• Consequence: PPIAP33 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0820
• 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 = 0.169 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: 0.164 AC: 24922 AN: 151996 Hom.: 2162 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.164 AC: 24932 AN: 152116 Hom.: 2162 Cov.: 32 AF XY: 0.164 AC XY: 12190 AN XY: 74362

African (AFR) AF: 0.168 AC: 6954 AN: 41492

American (AMR) AF: 0.141 AC: 2155 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 358 AN: 3468

East Asian (EAS) AF: 0.102 AC: 529 AN: 5186

South Asian (SAS) AF: 0.132 AC: 635 AN: 4822

European-Finnish (FIN) AF: 0.203 AC: 2148 AN: 10562

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11665 AN: 67976

Other (OTH) AF: 0.162 AC: 342 AN: 2112

Alfa AF: 0.165 Hom.: 5290

Bravo AF: 0.159

Asia WGS AF: 0.129 AC: 453 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	7.8
DANN	Benign	0.75
PhyloP100		-0.082

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4400445;

hg19: chr9-7558261;