rs61753111
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_014363.6(SACS):āc.9846A>Gā(p.Pro3282=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00382 in 1,613,892 control chromosomes in the GnomAD database, including 19 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. P3282P) 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 -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SACS | NM_014363.6 | c.9846A>G | p.Pro3282= | synonymous_variant | 10/10 | ENST00000382292.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SACS | ENST00000382292.9 | c.9846A>G | p.Pro3282= | synonymous_variant | 10/10 | 5 | NM_014363.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00271 AC: 413AN: 152206Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00292 AC: 733AN: 250882Hom.: 1 AF XY: 0.00294 AC XY: 399AN XY: 135578
GnomAD4 exome AF: 0.00393 AC: 5750AN: 1461568Hom.: 19 Cov.: 38 AF XY: 0.00390 AC XY: 2836AN XY: 727090
GnomAD4 genome ? AF: 0.00271 AC: 413AN: 152324Hom.: 0 Cov.: 33 AF XY: 0.00256 AC XY: 191AN XY: 74482
ClinVar
Submissions by phenotype
not provided Benign:5
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 03, 2020 | This variant is associated with the following publications: (PMID: 19779133) - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Dec 18, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | SACS: BP4, BP7 - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Spastic paraplegia Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Hereditary spastic paraplegia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Dec 08, 2020 | - - |
Charlevoix-Saguenay spastic ataxia Benign:1
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at