NM_006033.4:c.793+42T>C

Variant names:

• chr18-49575632-T-C
• rs2276269
• NM_006033.4:c.793+42T>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.793+42T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 1,533,108 control chromosomes in the GnomAD database, including 255,186 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 0.61 (29703 hom., cov: 30)
  • Exomes 𝑓: 0.57 (225483 hom.)
• Consequence: LIPG NM_006033.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• Publications: 21 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006033.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIPG	NM_006033.4	MANE Select	c.793+42T>C		intron	N/A	NP_006024.1
	LIPG	NM_001308006.2		c.572-5783T>C		intron	N/A	NP_001294935.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIPG	ENST00000261292.9	TSL:1 MANE Select	c.793+42T>C		intron	N/A	ENSP00000261292.4
	LIPG	ENST00000580036.5	TSL:1	c.793+42T>C		intron	N/A	ENSP00000462420.1
	LIPG	ENST00000427224.6	TSL:2	c.572-5783T>C		intron	N/A	ENSP00000387978.2

Frequencies

GnomAD3 genomes AF: 0.609 AC: 92509 AN: 151836 Hom.: 29669 Cov.: 30

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.745

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.622

GnomAD2 exomes AF: 0.547 AC: 126752 AN: 231804 AF XY: 0.558

Gnomad AFR exome AF: 0.813

Gnomad AMR exome AF: 0.368

Gnomad ASJ exome AF: 0.573

Gnomad EAS exome AF: 0.358

Gnomad FIN exome AF: 0.440

Gnomad NFE exome AF: 0.571

Gnomad OTH exome AF: 0.541

GnomAD4 exome AF: 0.565 AC: 780433 AN: 1381154 Hom.: 225483 Cov.: 20 AF XY: 0.570 AC XY: 393666 AN XY: 690540

African (AFR) AF: 0.821 AC: 26294 AN: 32026

American (AMR) AF: 0.375 AC: 16125 AN: 42952

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 14418 AN: 25532

East Asian (EAS) AF: 0.314 AC: 12287 AN: 39152

South Asian (SAS) AF: 0.682 AC: 57142 AN: 83774

European-Finnish (FIN) AF: 0.442 AC: 21666 AN: 49018

Middle Eastern (MID) AF: 0.751 AC: 4221 AN: 5622

European-Non Finnish (NFE) AF: 0.569 AC: 594999 AN: 1045318

Other (OTH) AF: 0.576 AC: 33281 AN: 57760

GnomAD4 genome AF: 0.609 AC: 92591 AN: 151954 Hom.: 29703 Cov.: 30 AF XY: 0.600 AC XY: 44567 AN XY: 74278

African (AFR) AF: 0.806 AC: 33405 AN: 41446

American (AMR) AF: 0.458 AC: 6989 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.564 AC: 1957 AN: 3468

East Asian (EAS) AF: 0.349 AC: 1799 AN: 5160

South Asian (SAS) AF: 0.674 AC: 3249 AN: 4818

European-Finnish (FIN) AF: 0.421 AC: 4434 AN: 10528

Middle Eastern (MID) AF: 0.740 AC: 216 AN: 292

European-Non Finnish (NFE) AF: 0.568 AC: 38601 AN: 67962

Other (OTH) AF: 0.622 AC: 1312 AN: 2108

Alfa AF: 0.586 Hom.: 81113

Bravo AF: 0.615

Asia WGS AF: 0.499 AC: 1734 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.54
DANN	Benign	0.74
PhyloP100		-1.8
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: rs2276269; hg19: chr18-47102002; COSMIC: COSV54294757;