rs654196
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000636183.2(CLN5):c.-262A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 1,328,844 control chromosomes in the GnomAD database, including 243,382 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.47 ( 20541 hom., cov: 32)
Exomes 𝑓: 0.60 ( 222841 hom. )
Consequence
CLN5
ENST00000636183.2 5_prime_UTR
ENST00000636183.2 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.412
Genes affected
CLN5 (HGNC:2076): (CLN5 intracellular trafficking protein) This gene is one of eight which have been associated with neuronal ceroid lipofuscinoses (NCL). Also referred to as Batten disease, NCL comprises a class of autosomal recessive, neurodegenerative disorders affecting children. The genes responsible likely encode proteins involved in the degradation of post-translationally modified proteins in lysosomes. The primary defect in NCL disorders is thought to be associated with lysosomal storage function.[provided by RefSeq, Oct 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=-0.79).
BP6
?
Variant 13-76991837-A-G is Benign according to our data. Variant chr13-76991837-A-G is described in ClinVar as [Benign]. Clinvar id is 670727.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLN5 | ENST00000636183.2 | c.-262A>G | 5_prime_UTR_variant | 1/4 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.467 AC: 71043AN: 151988Hom.: 20542 Cov.: 32
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GnomAD4 exome AF: 0.602 AC: 707938AN: 1176738Hom.: 222841 Cov.: 17 AF XY: 0.598 AC XY: 352312AN XY: 589576
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GnomAD4 genome ? AF: 0.467 AC: 71038AN: 152106Hom.: 20541 Cov.: 32 AF XY: 0.463 AC XY: 34406AN XY: 74354
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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 | Jun 14, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational 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