2-11370822-A-G

Position:

• chr2-11370822-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047446546.1(PPIAP60):​c.646-878A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.814 in 152,204 control chromosomes in the GnomAD database, including 50,811 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 0.81 (50811 hom., cov: 32)
• Consequence: PPIAP60 XM_047446546.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.71

Genes affected

PPIAP60 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PPIAP60	XM_047446546.1	c.646-878A>G		intron_variant			XP_047302502.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.814 AC: 123804 AN: 152086 Hom.: 50754 Cov.: 32

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.874

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.877

Gnomad MID AF: 0.787

Gnomad NFE AF: 0.855

Gnomad OTH AF: 0.787

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

GnomAD4 genome AF: 0.814 AC: 123923 AN: 152204 Hom.: 50811 Cov.: 32 AF XY: 0.814 AC XY: 60534 AN XY: 74408

Gnomad4 AFR AF: 0.747

Gnomad4 AMR AF: 0.875

Gnomad4 ASJ AF: 0.741

Gnomad4 EAS AF: 0.652

Gnomad4 SAS AF: 0.710

Gnomad4 FIN AF: 0.877

Gnomad4 NFE AF: 0.855

Gnomad4 OTH AF: 0.783

Alfa AF: 0.840 Hom.: 91328

Bravo AF: 0.811

Asia WGS AF: 0.676 AC: 2353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.036
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6716724; hg19: chr2-11510948;