rs6507931

Positions:

• chr18-49586638-C-T

Variant summary

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

The NM_006033.4(LIPG):​c.1377-108C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 775,888 control chromosomes in the GnomAD database, including 112,500 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Likely benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.52 (20992 hom., cov: 31)
  • Exomes 𝑓: 0.53 (91508 hom.)
• Consequence: LIPG NM_006033.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65

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=-0.82).
• BP6: Variant 18-49586638-C-T is Benign according to our data. Variant chr18-49586638-C-T is described in Lovd as [Likely_benign].
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LIPG	NM_006033.4	c.1377-108C>T		intron_variant		ENST00000261292.9
LIPG	NM_001308006.2	c.1155-108C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LIPG	ENST00000261292.9	c.1377-108C>T		intron_variant		1	NM_006033.4	P1
LIPG	ENST00000427224.6	c.1155-108C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78666 AN: 151862 Hom.: 20984 Cov.: 31

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.544

GnomAD4 exome AF: 0.528 AC: 329252 AN: 623906 Hom.: 91508 AF XY: 0.538 AC XY: 180554 AN XY: 335706

Gnomad4 AFR exome AF: 0.501

Gnomad4 AMR exome AF: 0.450

Gnomad4 ASJ exome AF: 0.560

Gnomad4 EAS exome AF: 0.111

Gnomad4 SAS exome AF: 0.648

Gnomad4 FIN exome AF: 0.433

Gnomad4 NFE exome AF: 0.564

Gnomad4 OTH exome AF: 0.528

GnomAD4 genome AF: 0.518 AC: 78703 AN: 151982 Hom.: 20992 Cov.: 31 AF XY: 0.512 AC XY: 38042 AN XY: 74268

Gnomad4 AFR AF: 0.497

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.634

Gnomad4 FIN AF: 0.419

Gnomad4 NFE AF: 0.566

Gnomad4 OTH AF: 0.542

Alfa AF: 0.558 Hom.: 13546

Bravo AF: 0.517

Asia WGS AF: 0.360 AC: 1252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.31
DANN	Benign	0.29

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs6507931; hg19: chr18-47113008;