rs1051339

Positions:

chr10-89247582-C-T

Variant summary

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

The ENST00000336233.10(LIPA):c.67G>A(p.Gly23Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 1,612,192 control chromosomes in the GnomAD database, including 9,505 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. G23G) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.13 ( 1590 hom., cov: 30)

Exomes 𝑓: 0.10 ( 7915 hom. )

Consequence

LIPA
ENST00000336233.10 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:12

Conservation

PhyloP100: -0.386

Variant links:

Genes affected

LIPA (HGNC:6617): (lipase A, lysosomal acid type) This gene encodes lipase A, the lysosomal acid lipase (also known as cholesterol ester hydrolase). This enzyme functions in the lysosome to catalyze the hydrolysis of cholesteryl esters and triglycerides. Mutations in this gene can result in Wolman disease and cholesteryl ester storage disease. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jan 2014]

LIPA 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 (MetaRNN=0.0035889745).

BP6

Variant 10-89247582-C-T is Benign according to our data. Variant chr10-89247582-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 255612.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-89247582-C-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
LIPA	NM_000235.4 linkuse as main transcript	c.67G>A	p.Gly23Arg	missense_variant	2/10	ENST00000336233.10	NP_000226.2
LIPA	NM_001127605.3 linkuse as main transcript	c.67G>A	p.Gly23Arg	missense_variant	2/10		NP_001121077.1
LIPA	XM_024448023.2 linkuse as main transcript	c.67G>A	p.Gly23Arg	missense_variant	2/10		XP_024303791.1
LIPA	NM_001288979.2 linkuse as main transcript	c.-120+4155G>A		intron_variant			NP_001275908.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LIPA	ENST00000336233.10 linkuse as main transcript	c.67G>A	p.Gly23Arg	missense_variant	2/10	1	NM_000235.4	ENSP00000337354	P1	P38571-1

Frequencies

GnomAD3 genomes

AF:

0.130

AC:

19710

AN:

151678

Hom.:

1588

Cov.:

show subpopulations

Gnomad AFR

AF:

0.222

Gnomad AMI

AF:

0.208

Gnomad AMR

AF:

0.101

Gnomad ASJ

AF:

0.0916

Gnomad EAS

AF:

0.0576

Gnomad SAS

AF:

0.0573

Gnomad FIN

AF:

0.0521

Gnomad MID

AF:

0.133

Gnomad NFE

AF:

0.104

Gnomad OTH

AF:

0.124

GnomAD3 exomes

AF:

0.0948

AC:

23828

AN:

251382

Hom.:

1432

AF XY:

0.0916

AC XY:

12450

AN XY:

135866

show subpopulations

Gnomad AFR exome

AF:

0.226

Gnomad AMR exome

AF:

0.0742

Gnomad ASJ exome

AF:

0.104

Gnomad EAS exome

AF:

0.0553

Gnomad SAS exome

AF:

0.0623

Gnomad FIN exome

AF:

0.0521

Gnomad NFE exome

AF:

0.104

Gnomad OTH exome

AF:

0.114

GnomAD4 exome

AF:

0.100

AC:

146658

AN:

1460396

Hom.:

7915

Cov.:

AF XY:

0.0989

AC XY:

71849

AN XY:

726598

show subpopulations

Gnomad4 AFR exome

AF:

0.221

Gnomad4 AMR exome

AF:

0.0770

Gnomad4 ASJ exome

AF:

0.0978

Gnomad4 EAS exome

AF:

0.0594

Gnomad4 SAS exome

AF:

0.0607

Gnomad4 FIN exome

AF:

0.0552

Gnomad4 NFE exome

AF:

0.104

Gnomad4 OTH exome

AF:

0.107

GnomAD4 genome

AF:

0.130

AC:

19722

AN:

151796

Hom.:

1590

Cov.:

AF XY:

0.125

AC XY:

9250

AN XY:

74200

show subpopulations

Gnomad4 AFR

AF:

0.222

Gnomad4 AMR

AF:

0.101

Gnomad4 ASJ

AF:

0.0916

Gnomad4 EAS

AF:

0.0576

Gnomad4 SAS

AF:

0.0567

Gnomad4 FIN

AF:

0.0521

Gnomad4 NFE

AF:

0.104

Gnomad4 OTH

AF:

0.123

Alfa

AF:

0.110

Hom.:

1799

Bravo

AF:

0.140

TwinsUK

AF:

0.102

AC:

380

ALSPAC

AF:

0.103

AC:

396

ESP6500AA

AF:

0.226

AC:

997

ESP6500EA

AF:

0.106

AC:

912

ExAC

AF:

0.101

AC:

12225

Asia WGS

AF:

0.0660

AC:

230

AN:

3478

EpiCase

AF:

0.108

EpiControl

AF:

0.111

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:12

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Lysosomal acid lipase deficiency

Benign:4

Benign, criteria provided, single submitter	clinical testing	GENinCode PLC	Jul 06, 2022	- -
Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 10, 2021	- -
Benign, no assertion criteria provided	clinical testing	Natera, Inc.	Nov 21, 2019	- -
Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 13, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

not provided

Benign:3

Benign, no assertion criteria provided	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Dec 15, 2015	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 03, 2015	This variant is associated with the following publications: (PMID: 31182375) -
Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:2

Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Likely benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Dec 03, 2021	- -

Wolman disease

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Likely benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jun 14, 2016	- -

Cardiovascular phenotype

Benign:1

Benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Feb 11, 2019

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.074

BayesDel_addAF

Benign

-0.53

BayesDel_noAF

Benign

-0.39

CADD

Benign

0.28

DANN

Benign

0.49

DEOGEN2

Benign

0.072

T;.;T

Eigen

Benign

-1.5

Eigen_PC

Benign

-1.5

FATHMM_MKL

Benign

0.0015

LIST_S2

Benign

0.22

T;T;T

MetaRNN

Benign

0.0036

T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.0

N;.;.

MutationTaster

Benign

1.0

P;P;P;P;P;P;P

PrimateAI

Benign

0.21

PROVEAN

Benign

-0.11

N;N;N

REVEL

Benign

0.13

Sift

Benign

0.59

T;T;T

Sift4G

Benign

0.58

T;.;.

Polyphen

0.0

B;.;.

Vest4

0.035

MutPred

0.12

Loss of glycosylation at S22 (P = 0.0317);Loss of glycosylation at S22 (P = 0.0317);Loss of glycosylation at S22 (P = 0.0317);

MPC

0.17

ClinPred

0.000031

GERP RS

-4.1

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Varity_R

0.031

gMVP

0.43

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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