rs193920982
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The ENST00000381535.4(SYNGR1):c.487-3C>T variant causes a splice region, splice polypyrimidine tract, intron change. The variant was absent in control chromosomes in GnomAD project. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Genomes: not found (cov: 33)
Consequence
SYNGR1
ENST00000381535.4 splice_region, splice_polypyrimidine_tract, intron
ENST00000381535.4 splice_region, splice_polypyrimidine_tract, intron
Scores
1
1
Splicing: ADA: 0.9083
2
Clinical Significance
Conservation
PhyloP100: 5.05
Genes affected
SYNGR1 (HGNC:11498): (synaptogyrin 1) This gene encodes an integral membrane protein associated with presynaptic vesicles in neuronal cells. The exact function of this protein is unclear, but studies of a similar murine protein suggest that it functions in synaptic plasticity without being required for synaptic transmission. The gene product belongs to the synaptogyrin gene family. Three alternatively spliced variants encoding three different isoforms have been identified. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SYNGR1 | NM_004711.5 | c.483+1398C>T | intron_variant | ENST00000328933.10 | |||
SYNGR1 | NM_145731.4 | c.484-3C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
SYNGR1 | NM_145738.3 | c.487-3C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYNGR1 | ENST00000328933.10 | c.483+1398C>T | intron_variant | 1 | NM_004711.5 | P1 | |||
SYNGR1 | ENST00000318801.8 | c.484-3C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | |||||
SYNGR1 | ENST00000381535.4 | c.487-3C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | |||||
SYNGR1 | ENST00000415332.1 | c.*156-3C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
GnomAD4 exome Cov.: 32
GnomAD4 exome
Cov.:
32
GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Malignant tumor of prostate Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | Science for Life laboratory, Karolinska Institutet | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at