20-45366988-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_033542.4(SYS1):c.344C>T(p.Ser115Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000415 in 1,614,206 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 Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. S115S) has been classified as Likely benign.
Frequency
Consequence
NM_033542.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SYS1 | NM_033542.4 | c.344C>T | p.Ser115Leu | missense_variant | 4/4 | ENST00000243918.10 | |
SYS1-DBNDD2 | NR_003189.2 | n.380+1302C>T | intron_variant, non_coding_transcript_variant | ||||
SYS1 | NM_001197129.2 | c.344C>T | p.Ser115Leu | missense_variant | 5/5 | ||
SYS1 | NM_001099791.3 | c.230+1302C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYS1 | ENST00000243918.10 | c.344C>T | p.Ser115Leu | missense_variant | 4/4 | 1 | NM_033542.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251488Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135918
GnomAD4 exome AF: 0.0000410 AC: 60AN: 1461886Hom.: 0 Cov.: 30 AF XY: 0.0000371 AC XY: 27AN XY: 727242
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152320Hom.: 0 Cov.: 32 AF XY: 0.0000268 AC XY: 2AN XY: 74496
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 22, 2023 | The c.344C>T (p.S115L) alteration is located in exon 5 (coding exon 3) of the SYS1 gene. This alteration results from a C to T substitution at nucleotide position 344, causing the serine (S) at amino acid position 115 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at