rs3738479

Variant names:

• chr1-151025366-T-A
• rs3738479
• NM_021222.3:c.521-149T>A

Variant summary

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

The NM_021222.3(PRUNE1):​c.521-149T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 723,754 control chromosomes in the GnomAD database, including 25,910 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 0.29 (7134 hom., cov: 31)
  • Exomes 𝑓: 0.25 (18776 hom.)
• Consequence: PRUNE1 NM_021222.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRUNE1	NM_021222.3	c.521-149T>A		intron_variant	Intron 4 of 7	ENST00000271620.8	NP_067045.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRUNE1	ENST00000271620.8	c.521-149T>A		intron_variant	Intron 4 of 7	1	NM_021222.3	ENSP00000271620.3

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44490 AN: 151926 Hom.: 7125 Cov.: 31

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.279

GnomAD4 exome AF: 0.245 AC: 140341 AN: 571710 Hom.: 18776 AF XY: 0.246 AC XY: 71360 AN XY: 289630

Gnomad4 AFR exome AF: 0.387

Gnomad4 AMR exome AF: 0.297

Gnomad4 ASJ exome AF: 0.189

Gnomad4 EAS exome AF: 0.405

Gnomad4 SAS exome AF: 0.348

Gnomad4 FIN exome AF: 0.230

Gnomad4 NFE exome AF: 0.223

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.293 AC: 44537 AN: 152044 Hom.: 7134 Cov.: 31 AF XY: 0.294 AC XY: 21868 AN XY: 74302

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.499

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.229

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.276

Alfa AF: 0.261 Hom.: 708

Bravo AF: 0.303

Asia WGS AF: 0.404 AC: 1407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.26
DANN	Benign	0.44

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: rs3738479; hg19: chr1-150997842;