10-116635787-A-T

Variant names:

• chr10-116635787-A-T
• rs1992824
• ENST00000579578.6:c.936+828A>T

Variant summary

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

The ENST00000579578.6(PNLIPRP2):​c.936+828A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 151,928 control chromosomes in the GnomAD database, including 6,133 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 0.27 (6133 hom., cov: 31)
• Consequence: PNLIPRP2 ENST00000579578.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 1 publications found

Genes affected

PNLIPRP2 (HGNC:9157): (pancreatic lipase related protein 2 (gene/pseudogene)) This gene encodes a lipase that hydrolyzes galactolipids, the main components of plant membrane lipids. An allelic polymorphism in this gene results in both coding and non-coding variants; the reference genome represents the non-coding allele. [provided by RefSeq, Aug 2015]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000579578.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PNLIPRP2	NR_103727.2		n.962+828A>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PNLIPRP2	ENST00000579578.6	TSL:2	c.936+828A>T		intron	N/A	ENSP00000463502.4
	PNLIPRP2	ENST00000588823.1	TSL:5	n.534+828A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40660 AN: 151810 Hom.: 6133 Cov.: 31

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.280

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.268 AC: 40662 AN: 151928 Hom.: 6133 Cov.: 31 AF XY: 0.267 AC XY: 19806 AN XY: 74236

African (AFR) AF: 0.120 AC: 4994 AN: 41448

American (AMR) AF: 0.274 AC: 4179 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.292 AC: 1014 AN: 3470

East Asian (EAS) AF: 0.292 AC: 1511 AN: 5178

South Asian (SAS) AF: 0.427 AC: 2055 AN: 4812

European-Finnish (FIN) AF: 0.258 AC: 2716 AN: 10508

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23286 AN: 67936

Other (OTH) AF: 0.279 AC: 590 AN: 2114

Alfa AF: 0.309 Hom.: 954

Bravo AF: 0.256

Asia WGS AF: 0.298 AC: 1036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.24
DANN	Benign	0.40
PhyloP100		-1.7

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

Other links and lift over

dbSNP: rs1992824; hg19: chr10-118395298;