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GeneBe

6-35795788-C-T

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

2

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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
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
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-2.67 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
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 UniProt
CLPSNM_001832.4 linkuse as main transcriptc.150G>A p.Ala50= synonymous_variant 2/3 ENST00000259938.7
CLPSNM_001252597.2 linkuse as main transcriptc.108G>A p.Ala36= synonymous_variant 3/4
CLPSNM_001252598.2 linkuse as main transcriptc.85-511G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CLPSENST00000259938.7 linkuse as main transcriptc.150G>A p.Ala50= synonymous_variant 2/31 NM_001832.4 P1
CLPSENST00000616014.3 linkuse as main transcriptc.85-511G>A intron_variant 1
CLPSENST00000622413.2 linkuse as main transcriptc.108G>A p.Ala36= synonymous_variant 2/35

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0175
AC:
2657
AN:
151460
Hom.:
0
Cov.:
40
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.:
0
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.:
0
Cov.:
32
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
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0176
AC:
2661
AN:
151576
Hom.:
0
Cov.:
40
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.:
0
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 submitterclinical testingInvitaeJul 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.

Other links and lift over

dbSNP: rs113528670; hg19: chr6-35763565; COSMIC: COSV52566107; COSMIC: COSV52566107; API