rs6432187

chr2-11354726-G-Achr2-11354726-G-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

PPIAP60 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
PPIAP60	XM_047446546.1	c.501+1117G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.488

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.291

Alfa AF: 0.273 Hom.: 7627

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6432187; hg19: chr2-11494852;