chr11-85704956-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_206927.4(SYTL2):c.6091C>T(p.Arg2031Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000341 in 1,613,336 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R2031H) has been classified as Uncertain significance.
Frequency
Consequence
NM_206927.4 missense
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 |
---|---|---|---|---|---|---|---|
SYTL2 | NM_206927.4 | c.6091C>T | p.Arg2031Cys | missense_variant | 16/20 | ENST00000359152.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYTL2 | ENST00000359152.10 | c.6091C>T | p.Arg2031Cys | missense_variant | 16/20 | 1 | NM_206927.4 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152106Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251372Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135864
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461230Hom.: 0 Cov.: 30 AF XY: 0.0000289 AC XY: 21AN XY: 726914
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152106Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74292
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 07, 2024 | The c.3190C>T (p.R1064C) alteration is located in exon 9 (coding exon 9) of the SYTL2 gene. This alteration results from a C to T substitution at nucleotide position 3190, causing the arginine (R) at amino acid position 1064 to be replaced by a cysteine (C). 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