rs2097055

Variant names:

• chr18-49569117-T-C
• rs2097055
• NM_006033.4:c.460-320T>C

Variant summary

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

The NM_006033.4(LIPG):​c.460-320T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 151,824 control chromosomes in the GnomAD database, including 23,640 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 0.55 (23640 hom., cov: 31)
• Consequence: LIPG NM_006033.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.222
• Publications: 10 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LIPG	NM_006033.4	c.460-320T>C		intron_variant	Intron 3 of 9	ENST00000261292.9	NP_006024.1
LIPG	NM_001308006.2	c.460-320T>C		intron_variant	Intron 3 of 8		NP_001294935.1
LIPG	XM_047437944.1	c.568-320T>C		intron_variant	Intron 3 of 4		XP_047293900.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LIPG	ENST00000261292.9	c.460-320T>C		intron_variant	Intron 3 of 9	1	NM_006033.4	ENSP00000261292.4
LIPG	ENST00000580036.5	c.460-320T>C		intron_variant	Intron 3 of 5	1		ENSP00000462420.1
LIPG	ENST00000427224.6	c.460-320T>C		intron_variant	Intron 3 of 8	2		ENSP00000387978.2
LIPG	ENST00000577628.5	c.568-320T>C		intron_variant	Intron 3 of 5	2		ENSP00000463835.1

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83517 AN: 151706 Hom.: 23621 Cov.: 31

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.589

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.550 AC: 83563 AN: 151824 Hom.: 23640 Cov.: 31 AF XY: 0.543 AC XY: 40267 AN XY: 74164

African (AFR) AF: 0.631 AC: 26099 AN: 41372

American (AMR) AF: 0.417 AC: 6357 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1906 AN: 3468

East Asian (EAS) AF: 0.350 AC: 1809 AN: 5166

South Asian (SAS) AF: 0.615 AC: 2962 AN: 4818

European-Finnish (FIN) AF: 0.424 AC: 4467 AN: 10524

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.558 AC: 37872 AN: 67910

Other (OTH) AF: 0.590 AC: 1243 AN: 2106

Alfa AF: 0.562 Hom.: 37763

Bravo AF: 0.547

Asia WGS AF: 0.464 AC: 1614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.6
DANN	Benign	0.42
PhyloP100		-0.22
Mutation Taster		=99/1	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: rs2097055; hg19: chr18-47095487;