rs755018918
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_198992.4(SYT10):c.1235G>A(p.Arg412Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000862 in 1,612,488 control chromosomes in the GnomAD database, including 1 homozygotes. 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 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SYT10 | ENST00000228567.7 | c.1235G>A | p.Arg412Gln | missense_variant | Exon 5 of 7 | 1 | NM_198992.4 | ENSP00000228567.3 | ||
SYT10 | ENST00000539102.1 | n.*830G>A | non_coding_transcript_exon_variant | Exon 7 of 9 | 1 | ENSP00000444577.1 | ||||
SYT10 | ENST00000539102.1 | n.*830G>A | 3_prime_UTR_variant | Exon 7 of 9 | 1 | ENSP00000444577.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152030Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000280 AC: 7AN: 249912Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135124
GnomAD4 exome AF: 0.0000931 AC: 136AN: 1460458Hom.: 1 Cov.: 31 AF XY: 0.0000867 AC XY: 63AN XY: 726562
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152030Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74232
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1235G>A (p.R412Q) alteration is located in exon 5 (coding exon 5) of the SYT10 gene. This alteration results from a G to A substitution at nucleotide position 1235, causing the arginine (R) at amino acid position 412 to be replaced by a glutamine (Q). 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