Variant chr18-49562371-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_006033.4(LIPG):c.63C>T(p.Ser21Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0112 in 1,613,570 control chromosomes in the GnomAD database, including 984 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.047 ( 505 hom., cov: 32)

Exomes 𝑓: 0.0075 ( 479 hom. )

Consequence

LIPG
NM_006033.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.116

Variant links:

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]

LIPG links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.72).

BP6

Variant 18-49562371-C-T is Benign according to our data. Variant chr18-49562371-C-T is described in ClinVar as [Benign]. Clinvar id is 1592089.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-49562371-C-T is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=0.116 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LIPG	NM_006033.4 linkuse as main transcript	c.63C>T	p.Ser21Ser	synonymous_variant	1/10	ENST00000261292.9	NP_006024.1	Q9Y5X9-1A0A024R2B5
LIPG	NM_001308006.2 linkuse as main transcript	c.63C>T	p.Ser21Ser	synonymous_variant	1/9		NP_001294935.1	Q9Y5X9B4DTR8
LIPG	XM_047437944.1 linkuse as main transcript	c.205+481C>T		intron_variant			XP_047293900.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LIPG	ENST00000261292.9 linkuse as main transcript	c.63C>T	p.Ser21Ser	synonymous_variant	1/10	1	NM_006033.4	ENSP00000261292.4		Q9Y5X9-1

Frequencies

GnomAD3 genomes

AF:

0.0465

AC:

7065

AN:

152016

Hom.:

506

Cov.:

show subpopulations

Gnomad AFR

AF:

0.150

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0270

Gnomad ASJ

AF:

0.0256

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00269

Gnomad FIN

AF:

0.000283

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.00351

Gnomad OTH

AF:

0.0412

GnomAD3 exomes

AF:

0.0152

AC:

3795

AN:

249294

Hom.:

196

AF XY:

0.0120

AC XY:

1621

AN XY:

134924

show subpopulations

Gnomad AFR exome

AF:

0.154

Gnomad AMR exome

AF:

0.0165

Gnomad ASJ exome

AF:

0.0225

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00101

Gnomad FIN exome

AF:

0.000185

Gnomad NFE exome

AF:

0.00341

Gnomad OTH exome

AF:

0.0121

GnomAD4 exome

AF:

0.00748

AC:

10929

AN:

1461436

Hom.:

479

Cov.:

AF XY:

0.00671

AC XY:

4876

AN XY:

726992

show subpopulations

Gnomad4 AFR exome

AF:

0.160

Gnomad4 AMR exome

AF:

0.0177

Gnomad4 ASJ exome

AF:

0.0225

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.000951

Gnomad4 FIN exome

AF:

0.0000936

Gnomad4 NFE exome

AF:

0.00267

Gnomad4 OTH exome

AF:

0.0165

GnomAD4 genome

AF:

0.0466

AC:

7084

AN:

152134

Hom.:

505

Cov.:

AF XY:

0.0445

AC XY:

3313

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.150

Gnomad4 AMR

AF:

0.0269

Gnomad4 ASJ

AF:

0.0256

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00290

Gnomad4 FIN

AF:

0.000283

Gnomad4 NFE

AF:

0.00351

Gnomad4 OTH

AF:

0.0408

Alfa

AF:

0.0267

Hom.:

117

Bravo

AF:

0.0544

Asia WGS

AF:

0.00924

AC:

AN:

3478

EpiCase

AF:

0.00447

EpiControl

AF:

0.00439

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

8.4

DANN

Benign

0.65

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over