rs754439135
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PM4_Supporting
The NM_014363.6(SACS):c.5149_5151del(p.Lys1717del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000175 in 1,605,954 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★). Synonymous variant affecting the same amino acid position (i.e. K1717K) has been classified as Likely benign.
Frequency
Consequence
NM_014363.6 inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SACS | NM_014363.6 | c.5149_5151del | p.Lys1717del | inframe_deletion | 10/10 | ENST00000382292.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SACS | ENST00000382292.9 | c.5149_5151del | p.Lys1717del | inframe_deletion | 10/10 | 5 | NM_014363.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151748Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000257 AC: 6AN: 233762Hom.: 0 AF XY: 0.0000237 AC XY: 3AN XY: 126598
GnomAD4 exome AF: 0.000191 AC: 278AN: 1454206Hom.: 0 AF XY: 0.000177 AC XY: 128AN XY: 723002
GnomAD4 genome ? AF: 0.0000198 AC: 3AN: 151748Hom.: 0 Cov.: 33 AF XY: 0.0000270 AC XY: 2AN XY: 74094
ClinVar
Submissions by phenotype
Hereditary spastic paraplegia Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Mar 01, 2018 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Apr 05, 2022 | - - |
Charlevoix-Saguenay spastic ataxia Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Jan 12, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at