XM_047446546.1:c.501+1117G>A

Variant names:

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

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPIAP60	XM_047446546.1	c.501+1117G>A		intron_variant	Intron 2 of 3		XP_047302502.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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

Other links and lift over

dbSNP: rs6432187; hg19: chr2-11494852;