chr13-23333208-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_014363.6(SACS):c.10668G>A(p.Leu3556=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000135 in 1,597,908 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. L3556L) has been classified as Likely benign.
Frequency
Consequence
NM_014363.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SACS | NM_014363.6 | c.10668G>A | p.Leu3556= | synonymous_variant | 10/10 | ENST00000382292.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SACS | ENST00000382292.9 | c.10668G>A | p.Leu3556= | synonymous_variant | 10/10 | 5 | NM_014363.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000690 AC: 105AN: 152110Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000137 AC: 32AN: 232952Hom.: 0 AF XY: 0.000103 AC XY: 13AN XY: 126070
GnomAD4 exome AF: 0.0000768 AC: 111AN: 1445680Hom.: 2 Cov.: 34 AF XY: 0.0000724 AC XY: 52AN XY: 717790
GnomAD4 genome AF: 0.000690 AC: 105AN: 152228Hom.: 0 Cov.: 33 AF XY: 0.000645 AC XY: 48AN XY: 74436
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Apr 17, 2017 | - - |
Likely benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Feb 29, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Oct 30, 2018 | - - |
Charlevoix-Saguenay spastic ataxia Benign:2
Likely benign, no assertion criteria provided | clinical testing | Natera, Inc. | Nov 11, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
Spastic paraplegia Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at