6-158763446-G-C
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_001242394.2(SYTL3):c.1660G>C(p.Val554Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,856 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V554F) has been classified as Uncertain significance.
Frequency
Consequence
NM_001242394.2 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SYTL3 | ENST00000611299.5 | c.1660G>C | p.Val554Leu | missense_variant | Exon 17 of 18 | 5 | NM_001242394.2 | ENSP00000483936.1 | ||
SYTL3 | ENST00000360448.8 | c.1660G>C | p.Val554Leu | missense_variant | Exon 18 of 19 | 5 | ENSP00000353631.4 | |||
SYTL3 | ENST00000367081.7 | c.1456G>C | p.Val486Leu | missense_variant | Exon 15 of 16 | 5 | ENSP00000356048.4 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD2 exomes AF: 0.00000398 AC: 1AN: 251494 AF XY: 0.00000736 show subpopulations
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461856Hom.: 0 Cov.: 34 AF XY: 0.00000138 AC XY: 1AN XY: 727238 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at