NM_198992.4:c.856C>T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_198992.4(SYT10):c.856C>T(p.Arg286Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00000805 in 1,613,928 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 (★).
Frequency
Consequence
NM_198992.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SYT10 | ENST00000228567.7 | c.856C>T | p.Arg286Cys | missense_variant | Exon 3 of 7 | 1 | NM_198992.4 | ENSP00000228567.3 | ||
SYT10 | ENST00000539102.1 | n.*451C>T | non_coding_transcript_exon_variant | Exon 5 of 9 | 1 | ENSP00000444577.1 | ||||
SYT10 | ENST00000539102.1 | n.*451C>T | 3_prime_UTR_variant | Exon 5 of 9 | 1 | ENSP00000444577.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152102Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251098Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135726
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461826Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 727200
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152102Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74308
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.856C>T (p.R286C) alteration is located in exon 3 (coding exon 3) of the SYT10 gene. This alteration results from a C to T substitution at nucleotide position 856, causing the arginine (R) at amino acid position 286 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