15-51686717-T-TTGTTCAACTGCAACTGGCTGGTGGACTTGGAACTTTTTTTTCTCTCACTTGCCTGGAAAAGTGCAAGGCAAGAACCTGAGAAACGAGCCTGTTATGCAGACCCAAATCATCCTTGCGATGGGC
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_013243.4(SCG3):c.398-1539_398-1538insCAACTGCAACTGGCTGGTGGACTTGGAACTTTTTTTTCTCTCACTTGCCTGGAAAAGTGCAAGGCAAGAACCTGAGAAACGAGCCTGTTATGCAGACCCAAATCATCCTTGCGATGGGCTGTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Genomes: not found (cov: 32)
Consequence
SCG3
NM_013243.4 intron
NM_013243.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -1.61
Genes affected
SCG3 (HGNC:13707): (secretogranin III) The protein encoded by this gene is a member of the chromogranin/secretogranin family of neuroendocrine secretory proteins. Granins may serve as precursors for biologically active peptides. Some granins have been shown to function as helper proteins in sorting and proteolytic processing of prohormones; however, the function of this protein is unknown. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]
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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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCG3 | NM_013243.4 | c.398-1539_398-1538insCAACTGCAACTGGCTGGTGGACTTGGAACTTTTTTTTCTCTCACTTGCCTGGAAAAGTGCAAGGCAAGAACCTGAGAAACGAGCCTGTTATGCAGACCCAAATCATCCTTGCGATGGGCTGTT | intron_variant | ENST00000220478.8 | NP_037375.2 | |||
SCG3 | NM_001165257.2 | c.-299-1539_-299-1538insCAACTGCAACTGGCTGGTGGACTTGGAACTTTTTTTTCTCTCACTTGCCTGGAAAAGTGCAAGGCAAGAACCTGAGAAACGAGCCTGTTATGCAGACCCAAATCATCCTTGCGATGGGCTGTT | intron_variant | NP_001158729.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCG3 | ENST00000220478.8 | c.398-1539_398-1538insCAACTGCAACTGGCTGGTGGACTTGGAACTTTTTTTTCTCTCACTTGCCTGGAAAAGTGCAAGGCAAGAACCTGAGAAACGAGCCTGTTATGCAGACCCAAATCATCCTTGCGATGGGCTGTT | intron_variant | 1 | NM_013243.4 | ENSP00000220478.3 | ||||
SCG3 | ENST00000542355.6 | c.-299-1539_-299-1538insCAACTGCAACTGGCTGGTGGACTTGGAACTTTTTTTTCTCTCACTTGCCTGGAAAAGTGCAAGGCAAGAACCTGAGAAACGAGCCTGTTATGCAGACCCAAATCATCCTTGCGATGGGCTGTT | intron_variant | 2 | ENSP00000445205.2 | |||||
SCG3 | ENST00000558709.1 | c.-156-2498_-156-2497insCAACTGCAACTGGCTGGTGGACTTGGAACTTTTTTTTCTCTCACTTGCCTGGAAAAGTGCAAGGCAAGAACCTGAGAAACGAGCCTGTTATGCAGACCCAAATCATCCTTGCGATGGGCTGTT | intron_variant | 2 | ENSP00000452745.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Schizophrenia Uncertain:1
Uncertain significance, no assertion criteria provided | case-control | Department of Psychiatry, The University of Hong Kong | Nov 11, 2022 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.