rs376432626
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_198992.4(SYT10):c.1420G>A(p.Glu474Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000434 in 1,613,850 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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.1420G>A | p.Glu474Lys | missense_variant | Exon 6 of 7 | 1 | NM_198992.4 | ENSP00000228567.3 | ||
SYT10 | ENST00000539102.1 | n.*1015G>A | non_coding_transcript_exon_variant | Exon 8 of 9 | 1 | ENSP00000444577.1 | ||||
SYT10 | ENST00000539102.1 | n.*1015G>A | 3_prime_UTR_variant | Exon 8 of 9 | 1 | ENSP00000444577.1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152138Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251358Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135836
GnomAD4 exome AF: 0.0000431 AC: 63AN: 1461712Hom.: 0 Cov.: 30 AF XY: 0.0000399 AC XY: 29AN XY: 727158
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152138Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1420G>A (p.E474K) alteration is located in exon 6 (coding exon 6) of the SYT10 gene. This alteration results from a G to A substitution at nucleotide position 1420, causing the glutamic acid (E) at amino acid position 474 to be replaced by a lysine (K). 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