dbSNP rs751039496: LIPE:p.Gly1073Val (chr19-42401825-C-A) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_005357.4(LIPE):c.3218G>T(p.Gly1073Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G1073E) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 30)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

LIPE
NM_005357.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.87

Publications

0 publications found

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:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.11663854).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005357.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
LIPE	NM_005357.4	MANE Select	c.3218G>T	p.Gly1073Val	missense	Exon 10 of 10	NP_005348.2
LIPE	NM_001416100.1		c.2468G>T	p.Gly823Val	missense	Exon 10 of 10	NP_001403029.1
LIPE	NM_001416101.1		c.2453G>T	p.Gly818Val	missense	Exon 10 of 10	NP_001403030.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
LIPE	ENST00000244289.9	TSL:1 MANE Select	c.3218G>T	p.Gly1073Val	missense	Exon 10 of 10	ENSP00000244289.3	Q05469-1
LIPE-AS1	ENST00000594624.8	TSL:1	n.105+4601C>A		intron	N/A
LIPE	ENST00000599918.2	TSL:5	c.3242G>T	p.Gly1081Val	missense	Exon 10 of 10	ENSP00000472218.2	M0R201

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1335512

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

656502

African (AFR)

AF:

0.00

AC:

AN:

28150

American (AMR)

AF:

0.00

AC:

AN:

27676

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

21494

East Asian (EAS)

AF:

0.00

AC:

AN:

33642

South Asian (SAS)

AF:

0.00

AC:

AN:

71034

European-Finnish (FIN)

AF:

0.00

AC:

AN:

40858

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3830

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1053408

Other (OTH)

AF:

0.00

AC:

AN:

55420

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.28

BayesDel_noAF

Benign

-0.64

CADD

Benign

(source)

DANN

Benign

0.97

DEOGEN2

Benign

0.039

Eigen

Benign

-0.65

Eigen_PC

Benign

-0.71

FATHMM_MKL

Benign

0.12

LIST_S2

Benign

0.38

M_CAP

Benign

0.015

MetaRNN

Benign

0.12

MetaSVM

Benign

-0.94

MutationAssessor

Benign

0.0

PhyloP100

1.9

PrimateAI

Uncertain

0.57

PROVEAN

Benign

-0.10

REVEL

Benign

0.060

Sift

Pathogenic

0.0

Polyphen

0.72

Vest4

0.14

MutPred

0.22

Loss of methylation at R1075 (P = 0.0417)

MVP

0.63

MPC

0.39

ClinPred

0.44

GERP RS

0.72

Varity_R

0.074

gMVP

0.29

Mutation Taster

=97/3

polymorphism

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over