rs7816032

chr8-19929380-C-T

Variant summary

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

The ENST00000520959.5(LPL):c.-140-18800C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 146,328 control chromosomes in the GnomAD database, including 11,076 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 0.33 (11076 hom., cov: 28)
• Consequence: LPL ENST00000520959.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.918

Genes affected

LPL (HGNC:6677): (lipoprotein lipase) LPL encodes lipoprotein lipase, which is expressed in heart, muscle, and adipose tissue. LPL functions as a homodimer, and has the dual functions of triglyceride hydrolase and ligand/bridging factor for receptor-mediated lipoprotein uptake. Severe mutations that cause LPL deficiency result in type I hyperlipoproteinemia, while less extreme mutations in LPL are linked to many disorders of lipoprotein metabolism. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LPL	ENST00000520959.5	c.-140-18800C>T		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.333 AC: 48688 AN: 146242 Hom.: 11049 Cov.: 28

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.333 AC: 48758 AN: 146328 Hom.: 11076 Cov.: 28 AF XY: 0.326 AC XY: 23249 AN XY: 71392

Gnomad4 AFR AF: 0.652

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.291

Alfa AF: 0.244 Hom.: 9115

Bravo AF: 0.357

Asia WGS AF: 0.255 AC: 884 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.40
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7816032; hg19: chr8-19786891;