rs6432187

Variant names:

• chr2-11354726-G-A
• rs6432187
• XM_047446546.1:c.501+1117G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-11354726-G-A
• chr2-11354726-G-C

Variant summary

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

The XM_047446546.1(PPIAP60):​c.501+1117G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 152,154 control chromosomes in the GnomAD database, including 5,299 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 0.25 (5299 hom., cov: 32)
• Consequence: PPIAP60 XM_047446546.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.809
• Publications: 4 publications found

Genes affected

PPIAP60 (HGNC:53684): (peptidylprolyl isomerase A pseudogene 60)

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 (EAS) allele frequency at 95% confidence interval = 0.472 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: 0.251 AC: 38099 AN: 152036 Hom.: 5300 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.251 AC: 38117 AN: 152154 Hom.: 5299 Cov.: 32 AF XY: 0.256 AC XY: 19012 AN XY: 74370

African (AFR) AF: 0.149 AC: 6195 AN: 41524

American (AMR) AF: 0.196 AC: 2999 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1154 AN: 3472

East Asian (EAS) AF: 0.488 AC: 2524 AN: 5170

South Asian (SAS) AF: 0.376 AC: 1807 AN: 4812

European-Finnish (FIN) AF: 0.344 AC: 3638 AN: 10576

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18794 AN: 67992

Other (OTH) AF: 0.291 AC: 615 AN: 2114

Alfa AF: 0.268 Hom.: 10556

Bravo AF: 0.237

Asia WGS AF: 0.411 AC: 1428 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	2.2
DANN	Benign	0.57
PhyloP100		0.81

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: rs6432187;

hg19: chr2-11494852;