rs7816032

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.918
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

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
LPLENST00000520959.5 linkuse as main transcriptc.-140-18800C>T intron_variant 4

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7816032; hg19: chr8-19786891; API