rs9951026

Positions:

• chr18-49583323-G-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The ENST00000261292.9(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 ENST00000261292.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.471

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]

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 18-49583323-G-A is Benign according to our data. Variant chr18-49583323-G-A is described in Lovd as [Benign].
• BA1: 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	Protein	UniProt
LIPG	NM_006033.4	c.1158-233G>A		intron_variant		ENST00000261292.9	NP_006024.1
LIPG	NM_001308006.2	c.936-233G>A		intron_variant			NP_001294935.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LIPG	ENST00000261292.9	c.1158-233G>A		intron_variant		1	NM_006033.4	ENSP00000261292	P1
LIPG	ENST00000427224.6	c.936-233G>A		intron_variant		2		ENSP00000387978

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74458 AN: 151760 Hom.: 18693 Cov.: 31

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 AF: 0.490 AC: 74489 AN: 151878 Hom.: 18703 Cov.: 31 AF XY: 0.484 AC XY: 35956 AN XY: 74230

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

Other links and lift over

dbSNP: rs9951026; hg19: chr18-47109693;