rs1325774
Positions:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006984.5(CLDN10):c.*11T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000441 in 1,361,388 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
Exomes 𝑓: 0.0000044 ( 0 hom. )
Consequence
CLDN10
NM_006984.5 3_prime_UTR
NM_006984.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0630
Genes affected
CLDN10 (HGNC:2033): (claudin 10) This gene encodes a member of the claudin family. Claudins are integral membrane proteins and components of tight junction strands. Tight junction strands serve as a physical barrier to prevent solutes and water from passing freely through the paracellular space between epithelial or endothelial cell sheets, and also play critical roles in maintaining cell polarity and signal transductions. The expression level of this gene is associated with recurrence of primary hepatocellular carcinoma. Six alternatively spliced transcript variants encoding different isoforms have been reported, but the transcript sequences of some variants are not determined.[provided by RefSeq, Jun 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLDN10 | NM_006984.5 | c.*11T>A | 3_prime_UTR_variant | 5/5 | ENST00000299339.3 | ||
CLDN10 | NM_001160100.2 | c.*11T>A | 3_prime_UTR_variant | 5/5 | |||
CLDN10 | NM_182848.4 | c.*11T>A | 3_prime_UTR_variant | 5/5 | |||
CLDN10 | XM_047430765.1 | c.*11T>A | 3_prime_UTR_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLDN10 | ENST00000299339.3 | c.*11T>A | 3_prime_UTR_variant | 5/5 | 1 | NM_006984.5 | P1 | ||
CLDN10 | ENST00000376873.7 | c.*11T>A | 3_prime_UTR_variant | 5/5 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
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32
GnomAD3 exomes AF: 0.0000167 AC: 4AN: 239476Hom.: 0 AF XY: 0.0000232 AC XY: 3AN XY: 129498
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GnomAD4 exome AF: 0.00000441 AC: 6AN: 1361388Hom.: 0 Cov.: 19 AF XY: 0.00000586 AC XY: 4AN XY: 682458
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GnomAD4 genome ? Cov.: 32
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32
ClinVar
Not reported inComputational scores
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Name
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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