dbSNP rs6507931: LIPG:c.1377-108C>T (chr18-49586638-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.52 ( 20992 hom., cov: 31)

Exomes 𝑓: 0.53 ( 91508 hom. )

Consequence

LIPG
NM_006033.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.65

Publications

14 publications found

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

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 rank	MANE	Protein	UniProt
LIPG	NM_006033.4 link	c.1377-108C>T		intron_variant	Intron 8 of 9	ENST00000261292.9	NP_006024.1	Q9Y5X9-1A0A024R2B5
LIPG	NM_001308006.2 link	c.1155-108C>T		intron_variant	Intron 7 of 8		NP_001294935.1	Q9Y5X9B4DTR8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LIPG	ENST00000261292.9 link	c.1377-108C>T		intron_variant	Intron 8 of 9	1	NM_006033.4	ENSP00000261292.4		Q9Y5X9-1
LIPG	ENST00000427224.6 link	c.1155-108C>T		intron_variant	Intron 7 of 8	2		ENSP00000387978.2		B4DTR8

Frequencies

GnomAD3 genomes

AF:

0.518

AC:

78666

AN:

151862

Hom.:

20984

Cov.:

show subpopulations

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

show subpopulations

African (AFR)

AF:

0.501

AC:

8845

AN:

17672

American (AMR)

AF:

0.450

AC:

16371

AN:

36364

Ashkenazi Jewish (ASJ)

AF:

0.560

AC:

11268

AN:

20118

East Asian (EAS)

AF:

0.111

AC:

3822

AN:

34570

South Asian (SAS)

AF:

0.648

AC:

42582

AN:

65678

European-Finnish (FIN)

AF:

0.433

AC:

21232

AN:

49090

Middle Eastern (MID)

AF:

0.725

AC:

2922

AN:

4030

European-Non Finnish (NFE)

AF:

0.564

AC:

205045

AN:

363846

Other (OTH)

AF:

0.528

AC:

17165

AN:

32538

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

7885

15770

23654

31539

39424

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1662

3324

4986

6648

8310

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.518

AC:

78703

AN:

151982

Hom.:

20992

Cov.:

AF XY:

0.512

AC XY:

38042

AN XY:

74268

show subpopulations

African (AFR)

AF:

0.497

AC:

20591

AN:

41432

American (AMR)

AF:

0.491

AC:

7501

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.561

AC:

1945

AN:

3468

East Asian (EAS)

AF:

0.141

AC:

727

AN:

5172

South Asian (SAS)

AF:

0.634

AC:

3054

AN:

4820

European-Finnish (FIN)

AF:

0.419

AC:

4424

AN:

10550

Middle Eastern (MID)

AF:

0.704

AC:

207

AN:

294

European-Non Finnish (NFE)

AF:

0.566

AC:

38480

AN:

67944

Other (OTH)

AF:

0.542

AC:

1142

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1913

3826

5740

7653

9566

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

704

1408

2112

2816

3520

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.546

Hom.:

22909

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

(source)

DANN

Benign

0.29

PhyloP100

-1.7

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over