Variant 9-133064589-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_001807.6(CEL):c.217+35G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0151 in 1,613,522 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.015 ( 5 hom., cov: 33)

Exomes 𝑓: 0.015 ( 6 hom. )

Consequence

CEL
NM_001807.6 intron

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.494

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 9-133064589-G-A is Benign according to our data. Variant chr9-133064589-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1179684.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.015 (2287/152220) while in subpopulation EAS AF= 0.0411 (212/5158). AF 95% confidence interval is 0.0366. There are 5 homozygotes in gnomad4. There are 1161 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High AC in GnomAd4 at 2287 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEL	NM_001807.6 linkuse as main transcript	c.217+35G>A		intron_variant		ENST00000372080.8	NP_001798.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEL	ENST00000372080.8 linkuse as main transcript	c.217+35G>A		intron_variant		5	NM_001807.6	ENSP00000361151	P1	P19835-1

Frequencies

GnomAD3 genomes

AF:

0.0150

AC:

2279

AN:

152102

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0149

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00471

Gnomad ASJ

AF:

0.0309

Gnomad EAS

AF:

0.0410

Gnomad SAS

AF:

0.0378

Gnomad FIN

AF:

0.0188

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0127

Gnomad OTH

AF:

0.0115

GnomAD3 exomes

AF:

0.0173

AC:

4295

AN:

248316

Hom.:

AF XY:

0.0190

AC XY:

2562

AN XY:

134964

show subpopulations

Gnomad AFR exome

AF:

0.0142

Gnomad AMR exome

AF:

0.00406

Gnomad ASJ exome

AF:

0.0246

Gnomad EAS exome

AF:

0.0382

Gnomad SAS exome

AF:

0.0376

Gnomad FIN exome

AF:

0.0187

Gnomad NFE exome

AF:

0.0121

Gnomad OTH exome

AF:

0.0144

GnomAD4 exome

AF:

0.0152

AC:

22154

AN:

1461302

Hom.:

Cov.:

AF XY:

0.0159

AC XY:

11564

AN XY:

726946

show subpopulations

Gnomad4 AFR exome

AF:

0.0162

Gnomad4 AMR exome

AF:

0.00436

Gnomad4 ASJ exome

AF:

0.0276

Gnomad4 EAS exome

AF:

0.0427

Gnomad4 SAS exome

AF:

0.0372

Gnomad4 FIN exome

AF:

0.0168

Gnomad4 NFE exome

AF:

0.0125

Gnomad4 OTH exome

AF:

0.0155

GnomAD4 genome

AF:

0.0150

AC:

2287

AN:

152220

Hom.:

Cov.:

AF XY:

0.0156

AC XY:

1161

AN XY:

74416

show subpopulations

Gnomad4 AFR

AF:

0.0150

Gnomad4 AMR

AF:

0.00471

Gnomad4 ASJ

AF:

0.0309

Gnomad4 EAS

AF:

0.0411

Gnomad4 SAS

AF:

0.0379

Gnomad4 FIN

AF:

0.0188

Gnomad4 NFE

AF:

0.0127

Gnomad4 OTH

AF:

0.0114

Alfa

AF:

0.0138

Hom.:

Bravo

AF:

0.0133

Asia WGS

AF:

0.0370

AC:

130

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 10, 2018	- -
Likely 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

-0.86

CADD

Benign

4.6

DANN

Benign

0.37

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