13-23375156-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP3BP6
The NM_014363.6(SACS):c.134C>T(p.Pro45Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000824 in 1,504,250 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. P45P) has been classified as Likely benign.
Frequency
Consequence
NM_014363.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SACS | NM_014363.6 | c.134C>T | p.Pro45Leu | missense_variant | 3/10 | ENST00000382292.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SACS | ENST00000382292.9 | c.134C>T | p.Pro45Leu | missense_variant | 3/10 | 5 | NM_014363.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 152032Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000300 AC: 3AN: 99918Hom.: 0 AF XY: 0.0000180 AC XY: 1AN XY: 55642
GnomAD4 exome AF: 0.0000873 AC: 118AN: 1352218Hom.: 0 Cov.: 32 AF XY: 0.0000870 AC XY: 58AN XY: 666836
GnomAD4 genome AF: 0.0000395 AC: 6AN: 152032Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74258
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jun 30, 2017 | - - |
Charlevoix-Saguenay spastic ataxia Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Nov 11, 2019 | - - |
Spastic paraplegia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 02, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at