X-38094418-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_138780.3(SYTL5):āc.955T>Cā(p.Ser319Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000037 in 1,082,496 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_138780.3 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 |
---|---|---|---|---|---|---|---|
SYTL5 | NM_138780.3 | c.955T>C | p.Ser319Pro | missense_variant | 8/17 | ENST00000297875.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYTL5 | ENST00000297875.7 | c.955T>C | p.Ser319Pro | missense_variant | 8/17 | 5 | NM_138780.3 | P4 | |
SYTL5 | ENST00000456733.2 | c.955T>C | p.Ser319Pro | missense_variant | 7/17 | 1 | A1 |
Frequencies
GnomAD3 genomes Cov.: 22
GnomAD3 exomes AF: 0.0000110 AC: 2AN: 182338Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 66972
GnomAD4 exome AF: 0.00000370 AC: 4AN: 1082496Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 350372
GnomAD4 genome Cov.: 22
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 07, 2022 | The c.955T>C (p.S319P) alteration is located in exon 8 (coding exon 7) of the SYTL5 gene. This alteration results from a T to C substitution at nucleotide position 955, causing the serine (S) at amino acid position 319 to be replaced by a proline (P). 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