chr1-42733444-A-G
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_148960.3(CLDN19):c.*1642T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,282 control chromosomes in the GnomAD database, including 3,009 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.19 ( 3006 hom., cov: 31)
Exomes 𝑓: 0.17 ( 3 hom. )
Consequence
CLDN19
NM_148960.3 3_prime_UTR
NM_148960.3 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.01
Genes affected
CLDN19 (HGNC:2040): (claudin 19) The product of this gene belongs to the claudin family. It plays a major role in tight junction-specific obliteration of the intercellular space, through calcium-independent cell-adhesion activity. Defects in this gene are the cause of hypomagnesemia renal with ocular involvement (HOMGO). HOMGO is a progressive renal disease characterized by primary renal magnesium wasting with hypomagnesemia, hypercalciuria and nephrocalcinosis associated with severe ocular abnormalities such as bilateral chorioretinal scars, macular colobomata, significant myopia and nystagmus. Alternatively spliced transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jun 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 1-42733444-A-G is Benign according to our data. Variant chr1-42733444-A-G is described in ClinVar as [Benign]. Clinvar id is 297318.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLDN19 | NM_148960.3 | c.*1642T>C | 3_prime_UTR_variant | 5/5 | ENST00000296387.6 | NP_683763.2 | ||
CLDN19 | NM_001123395.2 | c.*2424T>C | 3_prime_UTR_variant | 4/4 | NP_001116867.1 | |||
CLDN19 | NM_001185117.2 | c.*2318T>C | 3_prime_UTR_variant | 3/3 | NP_001172046.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CLDN19 | ENST00000296387.6 | c.*1642T>C | 3_prime_UTR_variant | 5/5 | 2 | NM_148960.3 | ENSP00000296387 | |||
CLDN19 | ENST00000539749.5 | c.*2318T>C | 3_prime_UTR_variant | 3/3 | 2 | ENSP00000443229 |
Frequencies
GnomAD3 genomes AF: 0.189 AC: 28777AN: 151982Hom.: 3000 Cov.: 31
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GnomAD4 exome AF: 0.170 AC: 31AN: 182Hom.: 3 Cov.: 0 AF XY: 0.191 AC XY: 26AN XY: 136
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GnomAD4 genome AF: 0.189 AC: 28805AN: 152100Hom.: 3006 Cov.: 31 AF XY: 0.185 AC XY: 13782AN XY: 74370
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Renal hypomagnesemia 5 with ocular involvement Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at