rs1867991

chr10-116592393-A-Cchr10-116592393-A-Gchr10-116592393-A-T

Variant summary

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

The NM_006229.4(PNLIPRP1):c.205-23A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.703 in 1,570,664 control chromosomes in the GnomAD database, including 389,833 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 0.67 (34843 hom., cov: 32)
  • Exomes 𝑓: 0.71 (354990 hom.)
• Consequence: PNLIPRP1 NM_006229.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

Genes affected

PNLIPRP1 (HGNC:9156): (pancreatic lipase related protein 1) Predicted to enable calcium ion binding activity. Predicted to be involved in lipid catabolic process. Predicted to be located in extracellular region. Biomarker of prostate cancer. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PNLIPRP1	NM_006229.4	c.205-23A>C		intron_variant		ENST00000358834.9
PNLIPRP1	NM_001303135.1	c.205-23A>C		intron_variant
PNLIPRP1	XM_047425364.1	c.205-23A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PNLIPRP1	ENST00000358834.9	c.205-23A>C		intron_variant		1	NM_006229.4	P4

Frequencies

GnomAD3 genomes AF: 0.675 AC: 102489 AN: 151928 Hom.: 34817 Cov.: 32

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.683

GnomAD3 exomes AF: 0.697 AC: 158080 AN: 226742 Hom.: 55485 AF XY: 0.699 AC XY: 85052 AN XY: 121726

Gnomad AFR exome AF: 0.602

Gnomad AMR exome AF: 0.739

Gnomad ASJ exome AF: 0.701

Gnomad EAS exome AF: 0.623

Gnomad SAS exome AF: 0.684

Gnomad FIN exome AF: 0.689

Gnomad NFE exome AF: 0.716

Gnomad OTH exome AF: 0.704

GnomAD4 exome AF: 0.706 AC: 1002231 AN: 1418618 Hom.: 354990 Cov.: 36 AF XY: 0.707 AC XY: 494669 AN XY: 700008

Gnomad4 AFR exome AF: 0.599

Gnomad4 AMR exome AF: 0.733

Gnomad4 ASJ exome AF: 0.703

Gnomad4 EAS exome AF: 0.625

Gnomad4 SAS exome AF: 0.690

Gnomad4 FIN exome AF: 0.696

Gnomad4 NFE exome AF: 0.714

Gnomad4 OTH exome AF: 0.699

GnomAD4 genome AF: 0.675 AC: 102567 AN: 152046 Hom.: 34843 Cov.: 32 AF XY: 0.675 AC XY: 50131 AN XY: 74314

Gnomad4 AFR AF: 0.601

Gnomad4 AMR AF: 0.688

Gnomad4 ASJ AF: 0.713

Gnomad4 EAS AF: 0.616

Gnomad4 SAS AF: 0.679

Gnomad4 FIN AF: 0.690

Gnomad4 NFE AF: 0.716

Gnomad4 OTH AF: 0.682

Alfa AF: 0.700 Hom.: 45000

Bravo AF: 0.671

Asia WGS AF: 0.621 AC: 2162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.96
Dann	Benign	0.35

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs1867991; hg19: chr10-118351905; COSMIC: COSV62610786; COSMIC: COSV62610786;