rs9951026

Variant names:

• chr18-49583323-G-A
• rs9951026
• NM_006033.4:c.1158-233G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.49 (18703 hom., cov: 31)
• Consequence: LIPG NM_006033.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.471
• Publications: 12 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• 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 rank	MANE	Protein	UniProt
LIPG	NM_006033.4	c.1158-233G>A		intron_variant	Intron 7 of 9	ENST00000261292.9	NP_006024.1
LIPG	NM_001308006.2	c.936-233G>A		intron_variant	Intron 6 of 8		NP_001294935.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LIPG	ENST00000261292.9	c.1158-233G>A		intron_variant	Intron 7 of 9	1	NM_006033.4	ENSP00000261292.4
LIPG	ENST00000427224.6	c.936-233G>A		intron_variant	Intron 6 of 8	2		ENSP00000387978.2

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

African (AFR) AF: 0.535 AC: 22117 AN: 41366

American (AMR) AF: 0.373 AC: 5690 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1740 AN: 3468

East Asian (EAS) AF: 0.330 AC: 1705 AN: 5160

South Asian (SAS) AF: 0.610 AC: 2930 AN: 4806

European-Finnish (FIN) AF: 0.380 AC: 4008 AN: 10552

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.507 AC: 34426 AN: 67934

Other (OTH) AF: 0.515 AC: 1088 AN: 2114

Alfa AF: 0.512 Hom.: 10331

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
PhyloP100		0.47
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9951026; hg19: chr18-47109693;