rs755740366
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1PM2
The ENST00000367255.10(SYNE1):c.19351C>T(p.Arg6451Ter) variant causes a stop gained change. The variant allele was found at a frequency of 0.00000186 in 1,613,598 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
ENST00000367255.10 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SYNE1 | NM_182961.4 | c.19351C>T | p.Arg6451Ter | stop_gained | 104/146 | ENST00000367255.10 | NP_892006.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SYNE1 | ENST00000367255.10 | c.19351C>T | p.Arg6451Ter | stop_gained | 104/146 | 1 | NM_182961.4 | ENSP00000356224 | P1 | |
SYNE1 | ENST00000423061.6 | c.19138C>T | p.Arg6380Ter | stop_gained | 103/146 | 1 | ENSP00000396024 | |||
SYNE1 | ENST00000367256.9 | n.3043C>T | non_coding_transcript_exon_variant | 19/61 | 1 | |||||
SYNE1 | ENST00000409694.6 | n.2935C>T | non_coding_transcript_exon_variant | 17/59 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152120Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250870Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135610
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461478Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727022
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152120Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74298
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at