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GeneBe

rs9951026

chr18-49583323-G-A

Variant summary

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

The NM_006033.4(LIPG):c.1158-233G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 151,878 control chromosomes in the GnomAD database, including 18,703 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).

Frequency

Genomes: 𝑓 0.49 ( 18703 hom., cov: 31)

Consequence

LIPG
NM_006033.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.471
Variant links:
Genes affected
LIPG (HGNC:6623): (lipase G, endothelial type) The protein encoded by this gene has substantial phospholipase activity and may be involved in lipoprotein metabolism and vascular biology. This protein is designated a member of the TG lipase family by its sequence and characteristic lid region which provides substrate specificity for enzymes of the TG lipase family. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

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=-0.84).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 18-49583323-G-A is Benign according to our data. Variant chr18-49583323-G-A 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 (SAS) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LIPGNM_006033.4 linkuse as main transcriptc.1158-233G>A intron_variant ENST00000261292.9
LIPGNM_001308006.2 linkuse as main transcriptc.936-233G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LIPGENST00000261292.9 linkuse as main transcriptc.1158-233G>A intron_variant 1 NM_006033.4 P1Q9Y5X9-1
LIPGENST00000427224.6 linkuse as main transcriptc.936-233G>A intron_variant 2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.491
AC:
74458
AN:
151760
Hom.:
18693
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.535
Gnomad AMI
AF:
0.660
Gnomad AMR
AF:
0.373
Gnomad ASJ
AF:
0.502
Gnomad EAS
AF:
0.331
Gnomad SAS
AF:
0.611
Gnomad FIN
AF:
0.380
Gnomad MID
AF:
0.633
Gnomad NFE
AF:
0.507
Gnomad OTH
AF:
0.514
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:
0.490
AC:
74489
AN:
151878
Hom.:
18703
Cov.:
31
AF XY:
0.484
AC XY:
35956
AN XY:
74230
show subpopulations
Gnomad4 AFR
AF:
0.535
Gnomad4 AMR
AF:
0.373
Gnomad4 ASJ
AF:
0.502
Gnomad4 EAS
AF:
0.330
Gnomad4 SAS
AF:
0.610
Gnomad4 FIN
AF:
0.380
Gnomad4 NFE
AF:
0.507
Gnomad4 OTH
AF:
0.515
Alfa
AF:
0.511
Hom.:
9199
Bravo
AF:
0.484
Asia WGS
AF:
0.428
AC:
1487
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
Cadd
Benign
8.0
Dann
Benign
0.67

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

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

Other links and lift over

dbSNP: rs9951026; hg19: chr18-47109693; API