Variant chr19-42402119-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_005357.4(LIPE):c.2968-44C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0979 in 1,423,346 control chromosomes in the GnomAD database, including 7,663 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.082 ( 648 hom., cov: 31)

Exomes 𝑓: 0.10 ( 7015 hom. )

Consequence

LIPE
NM_005357.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.0890

Variant links:

Genes affected

LIPE (HGNC:6621): (lipase E, hormone sensitive type) The protein encoded by this gene has a long and a short form, generated by use of alternative translational start codons. The long form is expressed in steroidogenic tissues such as testis, where it converts cholesteryl esters to free cholesterol for steroid hormone production. The short form is expressed in adipose tissue, among others, where it hydrolyzes stored triglycerides to free fatty acids. [provided by RefSeq, Jul 2008]

LIPE links:

LIPE-AS1 (HGNC:48589): (LIPE antisense RNA 1)

LIPE-AS1 links:

LOC101930071 (HGNC:):

LOC101930071 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 19-42402119-G-C is Benign according to our data. Variant chr19-42402119-G-C is described in ClinVar as [Benign]. Clinvar id is 1224184.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LIPE	NM_005357.4 link	c.2968-44C>G		intron_variant		ENST00000244289.9	NP_005348.2	Q05469-1A8K8W7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LIPE	ENST00000244289.9 link	c.2968-44C>G		intron_variant		1	NM_005357.4	ENSP00000244289.3		Q05469-1

Frequencies

GnomAD3 genomes

AF:

0.0825

AC:

12544

AN:

152130

Hom.:

652

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0318

Gnomad AMI

AF:

0.100

Gnomad AMR

AF:

0.125

Gnomad ASJ

AF:

0.0914

Gnomad EAS

AF:

0.0407

Gnomad SAS

AF:

0.196

Gnomad FIN

AF:

0.0739

Gnomad MID

AF:

0.225

Gnomad NFE

AF:

0.0986

Gnomad OTH

AF:

0.0929

GnomAD3 exomes

AF:

0.120

AC:

5293

AN:

43960

Hom.:

401

AF XY:

0.123

AC XY:

2813

AN XY:

22954

show subpopulations

Gnomad AFR exome

AF:

0.0333

Gnomad AMR exome

AF:

0.155

Gnomad ASJ exome

AF:

0.111

Gnomad EAS exome

AF:

0.0463

Gnomad SAS exome

AF:

0.217

Gnomad FIN exome

AF:

0.0750

Gnomad NFE exome

AF:

0.127

Gnomad OTH exome

AF:

0.113

GnomAD4 exome

AF:

0.0998

AC:

126798

AN:

1271098

Hom.:

7015

Cov.:

AF XY:

0.102

AC XY:

62843

AN XY:

615496

show subpopulations

Gnomad4 AFR exome

AF:

0.0301

Gnomad4 AMR exome

AF:

0.143

Gnomad4 ASJ exome

AF:

0.0897

Gnomad4 EAS exome

AF:

0.0308

Gnomad4 SAS exome

AF:

0.186

Gnomad4 FIN exome

AF:

0.0703

Gnomad4 NFE exome

AF:

0.0985

Gnomad4 OTH exome

AF:

0.101

GnomAD4 genome

AF:

0.0823

AC:

12530

AN:

152248

Hom.:

648

Cov.:

AF XY:

0.0841

AC XY:

6261

AN XY:

74444

show subpopulations

Gnomad4 AFR

AF:

0.0318

Gnomad4 AMR

AF:

0.125

Gnomad4 ASJ

AF:

0.0914

Gnomad4 EAS

AF:

0.0406

Gnomad4 SAS

AF:

0.195

Gnomad4 FIN

AF:

0.0739

Gnomad4 NFE

AF:

0.0985

Gnomad4 OTH

AF:

0.0915

Alfa

AF:

0.0909

Hom.:

Bravo

AF:

0.0835

Asia WGS

AF:

0.115

AC:

402

AN:

3478

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	GeneDx	Nov 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

5.9

DANN

Benign

0.38

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

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