rs3738480

Positions:

• chr1-151018349-A-G
• chr1-151018349-A-T

Variant summary

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

The NM_021222.3(PRUNE1):​c.133-118A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.754 in 890,738 control chromosomes in the GnomAD database, including 254,625 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 0.73 (41147 hom., cov: 31)
  • Exomes 𝑓: 0.76 (213478 hom.)
• Consequence: PRUNE1 NM_021222.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.494

Genes affected

PRUNE1 (HGNC:13420): (prune exopolyphosphatase 1) This gene encodes a member of the DHH protein superfamily of phosphoesterases. This protein has been found to function as both a nucleotide phosphodiesterase and an exopolyphosphatase. This protein is believed to stimulate cancer progression and metastases through the induction of cell motility. A pseuodgene has been identified on chromosome 13. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]

PRUNE1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.862 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRUNE1	NM_021222.3	c.133-118A>G		intron_variant		ENST00000271620.8	NP_067045.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRUNE1	ENST00000271620.8	c.133-118A>G		intron_variant		1	NM_021222.3	ENSP00000271620.3

Frequencies

GnomAD3 genomes AF: 0.734 AC: 111458 AN: 151850 Hom.: 41118 Cov.: 31

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.884

Gnomad SAS AF: 0.879

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.744

Gnomad OTH AF: 0.761

GnomAD3 exomes AF: 0.761 AC: 180098 AN: 236714 Hom.: 69111 AF XY: 0.771 AC XY: 99736 AN XY: 129402

Gnomad AFR exome AF: 0.714

Gnomad AMR exome AF: 0.678

Gnomad ASJ exome AF: 0.756

Gnomad EAS exome AF: 0.890

Gnomad SAS exome AF: 0.882

Gnomad FIN exome AF: 0.674

Gnomad NFE exome AF: 0.749

Gnomad OTH exome AF: 0.754

GnomAD4 exome AF: 0.758 AC: 559753 AN: 738770 Hom.: 213478 Cov.: 9 AF XY: 0.765 AC XY: 302503 AN XY: 395422

Gnomad4 AFR exome AF: 0.711

Gnomad4 AMR exome AF: 0.679

Gnomad4 ASJ exome AF: 0.756

Gnomad4 EAS exome AF: 0.874

Gnomad4 SAS exome AF: 0.881

Gnomad4 FIN exome AF: 0.676

Gnomad4 NFE exome AF: 0.746

Gnomad4 OTH exome AF: 0.752

GnomAD4 genome AF: 0.734 AC: 111546 AN: 151968 Hom.: 41147 Cov.: 31 AF XY: 0.732 AC XY: 54384 AN XY: 74264

Gnomad4 AFR AF: 0.714

Gnomad4 AMR AF: 0.681

Gnomad4 ASJ AF: 0.761

Gnomad4 EAS AF: 0.884

Gnomad4 SAS AF: 0.880

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.744

Gnomad4 OTH AF: 0.763

Alfa AF: 0.751 Hom.: 91661

Bravo AF: 0.733

Asia WGS AF: 0.847 AC: 2946 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	0.62
DANN	Benign	0.51

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3738480; hg19: chr1-150990825;