15-68208164-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_017882.3(CLN6):c.912C>T(p.Thr304=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000254 in 1,613,100 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. T304T) has been classified as Likely benign.
Frequency
Consequence
NM_017882.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLN6 | NM_017882.3 | c.912C>T | p.Thr304= | synonymous_variant | 7/7 | ENST00000249806.11 | |
CLN6 | NM_001411068.1 | c.1008C>T | p.Thr336= | synonymous_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLN6 | ENST00000249806.11 | c.912C>T | p.Thr304= | synonymous_variant | 7/7 | 1 | NM_017882.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000264 AC: 4AN: 151544Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000558 AC: 14AN: 251120Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135794
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1461438Hom.: 0 Cov.: 39 AF XY: 0.0000179 AC XY: 13AN XY: 727002
GnomAD4 genome AF: 0.0000264 AC: 4AN: 151662Hom.: 0 Cov.: 32 AF XY: 0.0000405 AC XY: 3AN XY: 74130
ClinVar
Submissions by phenotype
Neuronal ceroid lipofuscinosis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at