rs5934262
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The ENST00000650271.1(CLTRN):c.-506+1091A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.59 ( 13932 hom., 19684 hem., cov: 24)
Failed GnomAD Quality Control
Consequence
CLTRN
ENST00000650271.1 intron
ENST00000650271.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0880
Genes affected
CLTRN (HGNC:29437): (collectrin, amino acid transport regulator) This gene encodes a type 1 transmembrane protein that is important for trafficking amino acid transporters to the apical brush border of proximal tubules. The encoded protein binds to amino acid transporters and regulates their expression on the plasma membrane. It also plays a role in controlling insulin exocytosis by regulating formation of the SNARE (soluble N-ethylmaleimide-sensitive-factor attachment protein receptor) complex in pancreatic beta cells. The extracellular domain of the encoded protein may be cleaved and shed from the plasma membrane specifically in pancreatic beta cells. [provided by RefSeq, Jun 2013]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLTRN | XM_017029680.2 | c.-99+1545A>T | intron_variant | ||||
CLTRN | XM_024452411.2 | c.-99+1091A>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLTRN | ENST00000650271.1 | c.-506+1091A>T | intron_variant |
Frequencies
GnomAD3 genomes AF: 0.585 AC: 64940AN: 110991Hom.: 13914 Cov.: 24 AF XY: 0.591 AC XY: 19627AN XY: 33229
GnomAD3 genomes
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GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.586 AC: 65020AN: 111044Hom.: 13932 Cov.: 24 AF XY: 0.591 AC XY: 19684AN XY: 33292
GnomAD4 genome
Data not reliable, filtered out with message: InbreedingCoeff
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ClinVar
Not reported inComputational scores
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Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at