11-45255704-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020826.3(SYT13):c.371G>T(p.Arg124Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000204 in 1,614,008 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020826.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SYT13 | NM_020826.3 | c.371G>T | p.Arg124Met | missense_variant | 2/6 | ENST00000020926.8 | |
SYT13 | NM_001247987.2 | c.-62G>T | 5_prime_UTR_variant | 4/8 | |||
SYT13 | XM_047427338.1 | c.-62G>T | 5_prime_UTR_variant | 2/6 | |||
SYT13 | XM_047427339.1 | c.-62G>T | 5_prime_UTR_variant | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYT13 | ENST00000020926.8 | c.371G>T | p.Arg124Met | missense_variant | 2/6 | 1 | NM_020826.3 | P1 | |
SYT13 | ENST00000533332.1 | c.*388G>T | 3_prime_UTR_variant, NMD_transcript_variant | 4/8 | 1 | ||||
SYT13 | ENST00000528101.1 | c.251G>T | p.Arg84Met | missense_variant | 2/4 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152124Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250998Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135710
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461884Hom.: 0 Cov.: 31 AF XY: 0.0000206 AC XY: 15AN XY: 727246
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152124Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74322
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 17, 2022 | The c.371G>T (p.R124M) alteration is located in exon 2 (coding exon 2) of the SYT13 gene. This alteration results from a G to T substitution at nucleotide position 371, causing the arginine (R) at amino acid position 124 to be replaced by a methionine (M). 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