chr12-33376847-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_198992.4(SYT10):c.1555C>A(p.Pro519Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000235 in 1,613,990 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign 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 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SYT10 | ENST00000228567.7 | c.1555C>A | p.Pro519Thr | missense_variant | Exon 7 of 7 | 1 | NM_198992.4 | ENSP00000228567.3 | ||
SYT10 | ENST00000539102.1 | n.*1150C>A | non_coding_transcript_exon_variant | Exon 9 of 9 | 1 | ENSP00000444577.1 | ||||
SYT10 | ENST00000539102.1 | n.*1150C>A | 3_prime_UTR_variant | Exon 9 of 9 | 1 | ENSP00000444577.1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251282Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135800
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461822Hom.: 0 Cov.: 30 AF XY: 0.0000261 AC XY: 19AN XY: 727212
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74322
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1555C>A (p.P519T) alteration is located in exon 7 (coding exon 7) of the SYT10 gene. This alteration results from a C to A substitution at nucleotide position 1555, causing the proline (P) at amino acid position 519 to be replaced by a threonine (T). 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