rs148091182
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_198992.4(SYT10):āc.1015T>Cā(p.Phe339Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000178 in 1,613,886 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign 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 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SYT10 | ENST00000228567.7 | c.1015T>C | p.Phe339Leu | missense_variant | Exon 3 of 7 | 1 | NM_198992.4 | ENSP00000228567.3 | ||
SYT10 | ENST00000539102.1 | n.*610T>C | non_coding_transcript_exon_variant | Exon 5 of 9 | 1 | ENSP00000444577.1 | ||||
SYT10 | ENST00000539102.1 | n.*610T>C | 3_prime_UTR_variant | Exon 5 of 9 | 1 | ENSP00000444577.1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000598 AC: 15AN: 250942Hom.: 0 AF XY: 0.0000737 AC XY: 10AN XY: 135634
GnomAD4 exome AF: 0.000192 AC: 280AN: 1461694Hom.: 0 Cov.: 31 AF XY: 0.000180 AC XY: 131AN XY: 727136
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152192Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1015T>C (p.F339L) alteration is located in exon 3 (coding exon 3) of the SYT10 gene. This alteration results from a T to C substitution at nucleotide position 1015, causing the phenylalanine (F) at amino acid position 339 to be replaced by a leucine (L). 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