rs12696600
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_021101.5(CLDN1):c.-212G>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 594,924 control chromosomes in the GnomAD database, including 99,434 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.60 ( 28339 hom., cov: 34)
Exomes 𝑓: 0.56 ( 71095 hom. )
Consequence
CLDN1
NM_021101.5 5_prime_UTR
NM_021101.5 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.01
Genes affected
CLDN1 (HGNC:2032): (claudin 1) 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. The protein encoded by this gene, a member of the claudin family, is an integral membrane protein and a component of tight junction strands. Loss of function mutations result in neonatal ichthyosis-sclerosing cholangitis syndrome. [provided by RefSeq, Jul 2008]
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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=-0.69).
BP6
?
Variant 3-190322418-C-A is Benign according to our data. Variant chr3-190322418-C-A is described in ClinVar as [Benign]. Clinvar id is 1259600.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLDN1 | NM_021101.5 | c.-212G>T | 5_prime_UTR_variant | 1/4 | ENST00000295522.4 | ||
CLDN16 | NM_001378492.1 | c.-279+7359C>A | intron_variant | ||||
CLDN16 | NM_001378493.1 | c.-279+31827C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLDN1 | ENST00000295522.4 | c.-212G>T | 5_prime_UTR_variant | 1/4 | 1 | NM_021101.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.602 AC: 91471AN: 151982Hom.: 28318 Cov.: 34
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GnomAD4 exome AF: 0.561 AC: 248224AN: 442824Hom.: 71095 Cov.: 3 AF XY: 0.557 AC XY: 130024AN XY: 233324
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GnomAD4 genome ? AF: 0.602 AC: 91536AN: 152100Hom.: 28339 Cov.: 34 AF XY: 0.602 AC XY: 44741AN XY: 74342
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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 | GeneDx | Nov 10, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
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Benign
DANN
Benign
RBP_binding_hub_radar
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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