12-33382509-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_198992.4(SYT10):āc.1210A>Gā(p.Lys404Glu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000687 in 1,454,628 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 (ā ).
Frequency
Consequence
NM_198992.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SYT10 | ENST00000228567.7 | c.1210A>G | p.Lys404Glu | missense_variant | Exon 5 of 7 | 1 | NM_198992.4 | ENSP00000228567.3 | ||
SYT10 | ENST00000539102.1 | n.*805A>G | non_coding_transcript_exon_variant | Exon 7 of 9 | 1 | ENSP00000444577.1 | ||||
SYT10 | ENST00000539102.1 | n.*805A>G | 3_prime_UTR_variant | Exon 7 of 9 | 1 | ENSP00000444577.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000412 AC: 1AN: 242708Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 131350
GnomAD4 exome AF: 6.87e-7 AC: 1AN: 1454628Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 723634
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1210A>G (p.K404E) alteration is located in exon 5 (coding exon 5) of the SYT10 gene. This alteration results from a A to G substitution at nucleotide position 1210, causing the lysine (K) at amino acid position 404 to be replaced by a glutamic acid (E). 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