chr11-45244089-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_020826.3(SYT13):c.1244G>A(p.Arg415His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000213 in 1,609,066 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SYT13 | NM_020826.3 | c.1244G>A | p.Arg415His | missense_variant | Exon 6 of 6 | ENST00000020926.8 | NP_065877.1 | |
SYT13 | NM_001247987.2 | c.812G>A | p.Arg271His | missense_variant | Exon 8 of 8 | NP_001234916.1 | ||
SYT13 | XM_047427338.1 | c.812G>A | p.Arg271His | missense_variant | Exon 6 of 6 | XP_047283294.1 | ||
SYT13 | XM_047427339.1 | c.812G>A | p.Arg271His | missense_variant | Exon 6 of 6 | XP_047283295.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SYT13 | ENST00000020926.8 | c.1244G>A | p.Arg415His | missense_variant | Exon 6 of 6 | 1 | NM_020826.3 | ENSP00000020926.3 | ||
SYT13 | ENST00000533332.1 | n.*1261G>A | non_coding_transcript_exon_variant | Exon 8 of 8 | 1 | ENSP00000434967.1 | ||||
SYT13 | ENST00000533332.1 | n.*1261G>A | 3_prime_UTR_variant | Exon 8 of 8 | 1 | ENSP00000434967.1 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152140Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000121 AC: 30AN: 248642Hom.: 0 AF XY: 0.000104 AC XY: 14AN XY: 134560
GnomAD4 exome AF: 0.000224 AC: 326AN: 1456808Hom.: 0 Cov.: 31 AF XY: 0.000206 AC XY: 149AN XY: 724604
GnomAD4 genome AF: 0.000105 AC: 16AN: 152258Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74442
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1244G>A (p.R415H) alteration is located in exon 6 (coding exon 6) of the SYT13 gene. This alteration results from a G to A substitution at nucleotide position 1244, causing the arginine (R) at amino acid position 415 to be replaced by a histidine (H). 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