rs55724972
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_021101.5(CLDN1):c.*389G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0584 in 164,672 control chromosomes in the GnomAD database, including 361 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 0.058 ( 331 hom., cov: 32)
Exomes 𝑓: 0.063 ( 30 hom. )
Consequence
CLDN1
NM_021101.5 3_prime_UTR
NM_021101.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.420
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0802 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLDN1 | NM_021101.5 | c.*389G>T | 3_prime_UTR_variant | 4/4 | ENST00000295522.4 | ||
CLDN16 | NM_001378492.1 | c.-445-7005C>A | intron_variant | ||||
CLDN16 | NM_001378493.1 | c.-279+17297C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLDN1 | ENST00000295522.4 | c.*389G>T | 3_prime_UTR_variant | 4/4 | 1 | NM_021101.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0580 AC: 8811AN: 151884Hom.: 331 Cov.: 32
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GnomAD4 exome AF: 0.0632 AC: 801AN: 12670Hom.: 30 Cov.: 0 AF XY: 0.0640 AC XY: 452AN XY: 7060
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GnomAD4 genome ? AF: 0.0580 AC: 8812AN: 152002Hom.: 331 Cov.: 32 AF XY: 0.0569 AC XY: 4224AN XY: 74290
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at