chr6-31520368-A-G

Variant names:

• chr6-31520368-A-G
• rs3130637
• ENST00000403866.2:n.-77T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000403866.2(PPIAP9):​n.-77T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.786 in 660,704 control chromosomes in the GnomAD database, including 205,350 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 0.79 (47761 hom., cov: 32)
  • Exomes 𝑓: 0.78 (157589 hom.)
• Consequence: PPIAP9 ENST00000403866.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.769
• Publications: 34 publications found

Genes affected

PPIAP9 (HGNC:9272): (peptidylprolyl isomerase A pseudogene 9)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPIAP9	ENST00000403866.2	n.-77T>C		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.791 AC: 120286 AN: 151980 Hom.: 47720 Cov.: 32

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.859

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.860

Gnomad FIN AF: 0.810

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.787

GnomAD4 exome AF: 0.784 AC: 398684 AN: 508606 Hom.: 157589 AF XY: 0.789 AC XY: 214029 AN XY: 271214

African (AFR) AF: 0.824 AC: 10835 AN: 13144

American (AMR) AF: 0.805 AC: 19826 AN: 24642

Ashkenazi Jewish (ASJ) AF: 0.855 AC: 12355 AN: 14452

East Asian (EAS) AF: 0.901 AC: 28186 AN: 31268

South Asian (SAS) AF: 0.869 AC: 44958 AN: 51744

European-Finnish (FIN) AF: 0.795 AC: 32120 AN: 40416

Middle Eastern (MID) AF: 0.874 AC: 2424 AN: 2774

European-Non Finnish (NFE) AF: 0.749 AC: 226865 AN: 302934

Other (OTH) AF: 0.775 AC: 21115 AN: 27232

GnomAD4 genome AF: 0.791 AC: 120380 AN: 152098 Hom.: 47761 Cov.: 32 AF XY: 0.797 AC XY: 59268 AN XY: 74336

African (AFR) AF: 0.821 AC: 34056 AN: 41464

American (AMR) AF: 0.812 AC: 12402 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.859 AC: 2983 AN: 3472

East Asian (EAS) AF: 0.899 AC: 4659 AN: 5180

South Asian (SAS) AF: 0.861 AC: 4155 AN: 4824

European-Finnish (FIN) AF: 0.810 AC: 8556 AN: 10568

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.751 AC: 51043 AN: 67996

Other (OTH) AF: 0.789 AC: 1665 AN: 2110

Alfa AF: 0.771 Hom.: 175442

Bravo AF: 0.792

Asia WGS AF: 0.823 AC: 2864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.028
DANN	Benign	0.39
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs3130637; hg19: chr6-31488145;