8-1763883-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_018941.4(CLN8):c.-126C>T variant causes a splice region, 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0649 in 152,076 control chromosomes in the GnomAD database, including 441 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_018941.4 splice_region, 5_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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLN8 | NM_018941.4 | c.-126C>T | splice_region_variant, 5_prime_UTR_variant | 1/3 | ENST00000331222.6 | NP_061764.2 | ||
CLN8-AS1 | NR_134303.1 | n.151+551G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CLN8 | ENST00000331222.6 | c.-126C>T | splice_region_variant, 5_prime_UTR_variant | 1/3 | 1 | NM_018941.4 | ENSP00000328182 | P1 | ||
CLN8-AS1 | ENST00000659375.1 | n.75+551G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0649 AC: 9800AN: 150900Hom.: 441 Cov.: 28
GnomAD4 exome AF: 0.0675 AC: 72AN: 1066Hom.: 1 Cov.: 0 AF XY: 0.0625 AC XY: 50AN XY: 800
GnomAD4 genome AF: 0.0649 AC: 9796AN: 151010Hom.: 440 Cov.: 28 AF XY: 0.0700 AC XY: 5167AN XY: 73792
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 01, 2013 | 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. - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at