rs252

chr8-19953720-TA-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6 BA1

The NM_000237.3(LPL):c.541+302del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in Lovd as Likely benign (no stars).

• Frequency: Genomes: 𝑓 0.55 (25756 hom., cov: 0)
• Consequence: LPL NM_000237.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

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 -9 ACMG points.

• BP6: Variant 8-19953720-TA-T is Benign according to our data. Variant chr8-19953720-TA-T is described in Lovd as [Likely_benign].
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LPL	NM_000237.3	c.541+302del		intron_variant		ENST00000650287.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LPL	ENST00000650287.1	c.541+302del		intron_variant			NM_000237.3	P1
LPL	ENST00000520959.5	c.313+302del		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.553 AC: 84064 AN: 151886 Hom.: 25705 Cov.: 0

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.554 AC: 84162 AN: 152004 Hom.: 25756 Cov.: 0 AF XY: 0.547 AC XY: 40653 AN XY: 74270

Gnomad4 AFR AF: 0.831

Gnomad4 AMR AF: 0.469

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.346

Gnomad4 SAS AF: 0.406

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.491

Alfa AF: 0.517 Hom.: 2667

Bravo AF: 0.562

Asia WGS AF: 0.403 AC: 1402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs252; hg19: chr8-19811231;