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GeneBe

rs329

chr8-19962575-A-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_000237.3(LPL):c.1427+356A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0386 in 152,100 control chromosomes in the GnomAD database, including 163 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).

Frequency

Genomes: 𝑓 0.039 ( 163 hom., cov: 32)

Consequence

LPL
NM_000237.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0400
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 8-19962575-A-G is Benign according to our data. Variant chr8-19962575-A-G is described in Lovd as [Benign].
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0721 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LPLNM_000237.3 linkuse as main transcriptc.1427+356A>G intron_variant ENST00000650287.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LPLENST00000650287.1 linkuse as main transcriptc.1427+356A>G intron_variant NM_000237.3 P1
LPLENST00000650478.1 linkuse as main transcriptc.*250+356A>G intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0386
AC:
5871
AN:
151982
Hom.:
162
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0743
Gnomad AMI
AF:
0.0505
Gnomad AMR
AF:
0.0346
Gnomad ASJ
AF:
0.0651
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.0129
Gnomad FIN
AF:
0.0110
Gnomad MID
AF:
0.0665
Gnomad NFE
AF:
0.0252
Gnomad OTH
AF:
0.0403
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0386
AC:
5878
AN:
152100
Hom.:
163
Cov.:
32
AF XY:
0.0374
AC XY:
2782
AN XY:
74370
show subpopulations
Gnomad4 AFR
AF:
0.0743
Gnomad4 AMR
AF:
0.0346
Gnomad4 ASJ
AF:
0.0651
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.0127
Gnomad4 FIN
AF:
0.0110
Gnomad4 NFE
AF:
0.0252
Gnomad4 OTH
AF:
0.0399
Alfa
AF:
0.0302
Hom.:
11
Bravo
AF:
0.0424
Asia WGS
AF:
0.0110
AC:
39
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
Cadd
Benign
2.3
Dann
Benign
0.61

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

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

Other links and lift over

dbSNP: rs329; hg19: chr8-19820086; API