16-28477361-T-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001042432.2(CLN3):c.*155A>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 0.00254 in 990,702 control chromosomes in the GnomAD database, including 34 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001042432.2 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLN3 | NM_001042432.2 | c.*155A>C | 3_prime_UTR_variant | Exon 16 of 16 | ENST00000636147.2 | NP_001035897.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CLN3 | ENST00000636147 | c.*155A>C | 3_prime_UTR_variant | Exon 16 of 16 | 1 | NM_001042432.2 | ENSP00000490105.1 | |||
ENSG00000261832 | ENST00000637378.1 | c.228+4744A>C | intron_variant | Intron 4 of 9 | 5 | ENSP00000490831.1 |
Frequencies
GnomAD3 genomes AF: 0.0101 AC: 1530AN: 152148Hom.: 23 Cov.: 33
GnomAD4 exome AF: 0.00117 AC: 978AN: 838436Hom.: 11 Cov.: 11 AF XY: 0.000930 AC XY: 400AN XY: 430104
GnomAD4 genome AF: 0.0101 AC: 1540AN: 152266Hom.: 23 Cov.: 33 AF XY: 0.0100 AC XY: 748AN XY: 74456
ClinVar
Submissions by phenotype
not provided Benign:2
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Neuronal ceroid lipofuscinosis 3 Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at