ENST00000577628.5:c.-13A>C

Variant names:

• chr18-49561673-A-C
• rs3813082
• ENST00000577628.5:c.-13A>C

Variant summary

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

The ENST00000577628.5(LIPG):​c.-13A>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00769 in 1,239,728 control chromosomes in the GnomAD database, including 513 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 0.017 (110 hom., cov: 33)
  • Exomes 𝑓: 0.0063 (403 hom.)
• Consequence: LIPG ENST00000577628.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.579
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000577628.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIPG	ENST00000577628.5	TSL:2	c.-13A>C		5_prime_UTR	Exon 1 of 6	ENSP00000463835.1
	LIPG	ENST00000583083.1	TSL:3	c.-144+213A>C		intron	N/A	ENSP00000463077.1

Frequencies

GnomAD3 genomes AF: 0.0175 AC: 2656 AN: 152194 Hom.: 109 Cov.: 33

Gnomad AFR AF: 0.0298

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00536

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.0431

Gnomad FIN AF: 0.00226

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00112

Gnomad OTH AF: 0.0177

GnomAD2 exomes AF: 0.0189 AC: 48 AN: 2540 AF XY: 0.0156

Gnomad AFR exome AF: 0.0600

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.110

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00632 AC: 6871 AN: 1087416 Hom.: 403 Cov.: 30 AF XY: 0.00602 AC XY: 3090 AN XY: 513664

African (AFR) AF: 0.0311 AC: 715 AN: 22996

American (AMR) AF: 0.00233 AC: 24 AN: 10302

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14434

East Asian (EAS) AF: 0.143 AC: 3835 AN: 26848

South Asian (SAS) AF: 0.0398 AC: 804 AN: 20186

European-Finnish (FIN) AF: 0.00372 AC: 79 AN: 21210

Middle Eastern (MID) AF: 0.00445 AC: 13 AN: 2924

European-Non Finnish (NFE) AF: 0.000515 AC: 476 AN: 924540

Other (OTH) AF: 0.0210 AC: 925 AN: 43976

GnomAD4 genome AF: 0.0175 AC: 2663 AN: 152312 Hom.: 110 Cov.: 33 AF XY: 0.0189 AC XY: 1404 AN XY: 74472

African (AFR) AF: 0.0300 AC: 1246 AN: 41570

American (AMR) AF: 0.00536 AC: 82 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.191 AC: 987 AN: 5168

South Asian (SAS) AF: 0.0427 AC: 206 AN: 4824

European-Finnish (FIN) AF: 0.00226 AC: 24 AN: 10626

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.00112 AC: 76 AN: 68024

Other (OTH) AF: 0.0194 AC: 41 AN: 2116

Alfa AF: 0.00418 Hom.: 0

Bravo AF: 0.0188

Asia WGS AF: 0.105 AC: 365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	10
DANN	Benign	0.54
PhyloP100		0.58
PromoterAI		0.0059	Neutral
Mutation Taster		=299/1	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3813082; hg19: chr18-47088043;