XM_047446546.1:c.646-878A>G

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.

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: 0.814 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 v4.9

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;