rs2717701
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_021195.5(CLDN6):c.-21-125C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 813,862 control chromosomes in the GnomAD database, including 58,055 homozygotes. 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 0.36 ( 10078 hom., cov: 33)
Exomes 𝑓: 0.37 ( 47977 hom. )
Consequence
CLDN6
NM_021195.5 intron
NM_021195.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.811
Genes affected
CLDN6 (HGNC:2048): (claudin 6) Tight junctions represent one mode of cell-to-cell adhesion in epithelial or endothelial cell sheets, forming continuous seals around cells and serving as a physical barrier to prevent solutes and water from passing freely through the paracellular space. These junctions are comprised of sets of continuous networking strands in the outwardly facing cytoplasmic leaflet, with complementary grooves in the inwardly facing extracytoplasmic leaflet. This gene encodes a component of tight junction strands, which is a member of the claudin family. The protein is an integral membrane protein and is one of the entry cofactors for hepatitis C virus. The gene methylation may be involved in esophageal tumorigenesis. This gene is adjacent to another family member CLDN9 on chromosome 16.[provided by RefSeq, Aug 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLDN6 | NM_021195.5 | c.-21-125C>G | intron_variant | ENST00000328796.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLDN6 | ENST00000328796.5 | c.-21-125C>G | intron_variant | 1 | NM_021195.5 | P1 | |||
CLDN6 | ENST00000396925.1 | c.-21-125C>G | intron_variant | 5 | P1 | ||||
CLDN6 | ENST00000572154.1 | c.-21-125C>G | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.357 AC: 54273AN: 152014Hom.: 10071 Cov.: 33
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GnomAD4 exome AF: 0.374 AC: 247547AN: 661730Hom.: 47977 AF XY: 0.371 AC XY: 125049AN XY: 337068
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GnomAD4 genome ? AF: 0.357 AC: 54292AN: 152132Hom.: 10078 Cov.: 33 AF XY: 0.351 AC XY: 26064AN XY: 74356
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ClinVar
Not reported inComputational 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