rs6716724

Variant names:

• chr2-11370822-A-G
• rs6716724
• XM_047446546.1:c.646-878A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 16 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=-0.83).
• 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 rank	MANE	Protein	UniProt
PPIAP60	XM_047446546.1	c.646-878A>G		intron_variant	Intron 3 of 3		XP_047302502.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.747 AC: 31023 AN: 41526

American (AMR) AF: 0.875 AC: 13377 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.741 AC: 2571 AN: 3468

East Asian (EAS) AF: 0.652 AC: 3374 AN: 5174

South Asian (SAS) AF: 0.710 AC: 3418 AN: 4816

European-Finnish (FIN) AF: 0.877 AC: 9300 AN: 10602

Middle Eastern (MID) AF: 0.781 AC: 228 AN: 292

European-Non Finnish (NFE) AF: 0.855 AC: 58151 AN: 68004

Other (OTH) AF: 0.783 AC: 1656 AN: 2114

Alfa AF: 0.839 Hom.: 102106

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
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs6716724; hg19: chr2-11510948;