Variant chr9-133071566-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_001807.6(CEL):c.2064C>G(p.Gly688Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0083 ( 2 hom., cov: 0)

Exomes 𝑓: 0.0049 ( 9 hom. )

Failed GnomAD Quality Control

Consequence

CEL
NM_001807.6 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.330

Variant links:

Genes affected

CEL (HGNC:1848): (carboxyl ester lipase) The protein encoded by this gene is a glycoprotein secreted from the pancreas into the digestive tract and from the lactating mammary gland into human milk. The physiological role of this protein is in cholesterol and lipid-soluble vitamin ester hydrolysis and absorption. This encoded protein promotes large chylomicron production in the intestine. Also its presence in plasma suggests its interactions with cholesterol and oxidized lipoproteins to modulate the progression of atherosclerosis. In pancreatic tumoral cells, this encoded protein is thought to be sequestrated within the Golgi compartment and is probably not secreted. This gene contains a variable number of tandem repeat (VNTR) polymorphism in the coding region that may influence the function of the encoded protein. [provided by RefSeq, Jul 2008]

CEL links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 9-133071566-C-G is Benign according to our data. Variant chr9-133071566-C-G is described in ClinVar as [Benign]. Clinvar id is 128690.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-133071566-C-G is described in Lovd as [Likely_benign]. Variant chr9-133071566-C-G is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=0.33 with no splicing effect.

BS2

High AC in GnomAd4 at 316 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEL	NM_001807.6 linkuse as main transcript	c.2064C>G	p.Gly688Gly	synonymous_variant	11/11	ENST00000372080.8	NP_001798.3	B4DSX9Q86SR3O75612

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEL	ENST00000372080.8 linkuse as main transcript	c.2064C>G	p.Gly688Gly	synonymous_variant	11/11	5	NM_001807.6	ENSP00000361151.6		P19835-1

Frequencies

GnomAD3 genomes

AF:

0.00835

AC:

316

AN:

37866

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00692

Gnomad AMI

AF:

0.00758

Gnomad AMR

AF:

0.0126

Gnomad ASJ

AF:

0.0224

Gnomad EAS

AF:

0.00744

Gnomad SAS

AF:

0.00154

Gnomad FIN

AF:

0.00711

Gnomad MID

AF:

0.0217

Gnomad NFE

AF:

0.00844

Gnomad OTH

AF:

0.0132

GnomAD3 exomes

AF:

0.00451

AC:

298

AN:

66008

Hom.:

AF XY:

0.00509

AC XY:

191

AN XY:

37518

show subpopulations

Gnomad AFR exome

AF:

0.000821

Gnomad AMR exome

AF:

0.00418

Gnomad ASJ exome

AF:

0.0105

Gnomad EAS exome

AF:

0.00306

Gnomad SAS exome

AF:

0.00192

Gnomad FIN exome

AF:

0.00874

Gnomad NFE exome

AF:

0.00639

Gnomad OTH exome

AF:

0.00106

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00492

AC:

2562

AN:

520650

Hom.:

Cov.:

AF XY:

0.00502

AC XY:

1346

AN XY:

268290

show subpopulations

Gnomad4 AFR exome

AF:

0.00207

Gnomad4 AMR exome

AF:

0.00386

Gnomad4 ASJ exome

AF:

0.00891

Gnomad4 EAS exome

AF:

0.00252

Gnomad4 SAS exome

AF:

0.00132

Gnomad4 FIN exome

AF:

0.00482

Gnomad4 NFE exome

AF:

0.00576

Gnomad4 OTH exome

AF:

0.00352

GnomAD4 genome

AF:

0.00834

AC:

316

AN:

37878

Hom.:

Cov.:

AF XY:

0.00879

AC XY:

163

AN XY:

18546

show subpopulations

Gnomad4 AFR

AF:

0.00699

Gnomad4 AMR

AF:

0.0126

Gnomad4 ASJ

AF:

0.0224

Gnomad4 EAS

AF:

0.00679

Gnomad4 SAS

AF:

0.00155

Gnomad4 FIN

AF:

0.00711

Gnomad4 NFE

AF:

0.00844

Gnomad4 OTH

AF:

0.0132

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Benign, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -
Benign, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Feb 14, 2014	- -

not provided

Benign:2

Likely benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.92

DANN

Benign

0.63

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