chr6-158760641-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001242394.2(SYTL3):c.1310C>T(p.Ala437Val) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000347 in 1,613,458 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 17/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001242394.2 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SYTL3 | NM_001242394.2 | c.1310C>T | p.Ala437Val | missense_variant, splice_region_variant | 15/18 | ENST00000611299.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYTL3 | ENST00000611299.5 | c.1310C>T | p.Ala437Val | missense_variant, splice_region_variant | 15/18 | 5 | NM_001242394.2 | P1 | |
SYTL3 | ENST00000360448.8 | c.1310C>T | p.Ala437Val | missense_variant, splice_region_variant | 16/19 | 5 | P1 | ||
SYTL3 | ENST00000367081.7 | c.1106C>T | p.Ala369Val | missense_variant, splice_region_variant | 13/16 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152098Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251420Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135880
GnomAD4 exome AF: 0.0000308 AC: 45AN: 1461242Hom.: 0 Cov.: 30 AF XY: 0.0000303 AC XY: 22AN XY: 726988
GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152216Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74400
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 08, 2023 | The c.1310C>T (p.A437V) alteration is located in exon 15 (coding exon 12) of the SYTL3 gene. This alteration results from a C to T substitution at nucleotide position 1310, causing the alanine (A) at amino acid position 437 to be replaced by a valine (V). 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