chr6-35796793-G-A
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001832.4(CLPS):c.84+412C>T variant causes a intron 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 0.25 ( 486 hom., cov: 45)
Exomes 𝑓: 0.15 ( 145 hom. )
Failed GnomAD Quality Control
Consequence
CLPS
NM_001832.4 intron
NM_001832.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.968
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 -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
Variant 6-35796793-G-A is Benign according to our data. Variant chr6-35796793-G-A is described in ClinVar as [Benign]. Clinvar id is 402546.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLPS | NM_001832.4 | c.84+412C>T | intron_variant | ENST00000259938.7 | NP_001823.1 | |||
CLPS | NM_001252597.2 | c.42+16C>T | intron_variant | NP_001239526.1 | ||||
CLPS | NM_001252598.2 | c.84+412C>T | intron_variant | NP_001239527.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CLPS | ENST00000259938.7 | c.84+412C>T | intron_variant | 1 | NM_001832.4 | ENSP00000259938.2 | ||||
CLPS | ENST00000616014.3 | c.84+412C>T | intron_variant | 1 | ENSP00000483589.1 | |||||
CLPS | ENST00000622413.2 | c.42+16C>T | intron_variant | 5 | ENSP00000482919.1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 36841AN: 146996Hom.: 482 Cov.: 45 FAILED QC
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GnomAD3 exomes AF: 0.142 AC: 15003AN: 105302Hom.: 77 AF XY: 0.138 AC XY: 7978AN XY: 57726
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GnomAD4 exome AF: 0.150 AC: 38557AN: 256718Hom.: 145 Cov.: 0 AF XY: 0.145 AC XY: 21348AN XY: 146842
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GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.251 AC: 36884AN: 147110Hom.: 486 Cov.: 45 AF XY: 0.247 AC XY: 17782AN XY: 71888
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at