Variant 6-35795788-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001832.4(CLPS):c.150G>A(p.Ala50=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00399 in 1,610,678 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.018 ( 0 hom., cov: 40)

Exomes 𝑓: 0.0026 ( 0 hom. )

Consequence

CLPS
NM_001832.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.67

Variant links:

Genes affected

CLPS (HGNC:2085): (colipase) The protein encoded by this gene is a cofactor needed by pancreatic lipase for efficient dietary lipid hydrolysis. It binds to the C-terminal, non-catalytic domain of lipase, thereby stabilizing an active conformation and considerably increasing the overall hydrophobic binding site. The gene product allows lipase to anchor noncovalently to the surface of lipid micelles, counteracting the destabilizing influence of intestinal bile salts. This cofactor is only expressed in pancreatic acinar cells, suggesting regulation of expression by tissue-specific elements. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]

CLPS links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP6

Variant 6-35795788-C-T is Benign according to our data. Variant chr6-35795788-C-T is described in ClinVar as [Benign]. Clinvar id is 780119.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-2.67 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
CLPS	NM_001832.4 linkuse as main transcript	c.150G>A	p.Ala50=	synonymous_variant	2/3	ENST00000259938.7	NP_001823.1
CLPS	NM_001252597.2 linkuse as main transcript	c.108G>A	p.Ala36=	synonymous_variant	3/4		NP_001239526.1
CLPS	NM_001252598.2 linkuse as main transcript	c.85-511G>A		intron_variant			NP_001239527.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
CLPS	ENST00000259938.7 linkuse as main transcript	c.150G>A	p.Ala50=	synonymous_variant	2/3	1	NM_001832.4	ENSP00000259938	P1
CLPS	ENST00000616014.3 linkuse as main transcript	c.85-511G>A		intron_variant		1		ENSP00000483589
CLPS	ENST00000622413.2 linkuse as main transcript	c.108G>A	p.Ala36=	synonymous_variant	2/3	5		ENSP00000482919

Frequencies

GnomAD3 genomes

AF:

0.0175

AC:

2657

AN:

151460

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0568

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00793

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0250

Gnomad SAS

AF:

0.00290

Gnomad FIN

AF:

0.0000941

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.000426

Gnomad OTH

AF:

0.0197

GnomAD3 exomes

AF:

0.00542

AC:

1354

AN:

249594

Hom.:

AF XY:

0.00414

AC XY:

559

AN XY:

135026

show subpopulations

Gnomad AFR exome

AF:

0.0493

Gnomad AMR exome

AF:

0.00333

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0199

Gnomad SAS exome

AF:

0.00167

Gnomad FIN exome

AF:

0.0000956

Gnomad NFE exome

AF:

0.000255

Gnomad OTH exome

AF:

0.00343

GnomAD4 exome

AF:

0.00258

AC:

3767

AN:

1459102

Hom.:

Cov.:

AF XY:

0.00229

AC XY:

1663

AN XY:

725882

show subpopulations

Gnomad4 AFR exome

AF:

0.0538

Gnomad4 AMR exome

AF:

0.00401

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0290

Gnomad4 SAS exome

AF:

0.00117

Gnomad4 FIN exome

AF:

0.000286

Gnomad4 NFE exome

AF:

0.000142

Gnomad4 OTH exome

AF:

0.00644

GnomAD4 genome

AF:

0.0176

AC:

2661

AN:

151576

Hom.:

Cov.:

AF XY:

0.0168

AC XY:

1242

AN XY:

74126

show subpopulations

Gnomad4 AFR

AF:

0.0567

Gnomad4 AMR

AF:

0.00792

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0249

Gnomad4 SAS

AF:

0.00290

Gnomad4 FIN

AF:

0.0000941

Gnomad4 NFE

AF:

0.000426

Gnomad4 OTH

AF:

0.0210

Alfa

AF:

0.00434

Hom.:

Asia WGS

AF:

0.0380

AC:

131

AN:

3478

EpiCase

AF:

0.000109

EpiControl

AF:

0.0000593

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jul 27, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

1.4

DANN

Benign

0.49

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