15-51686717-T-TTGTTCAACTGCAACTGGCTGGTGGACTTGGAACTTTTTTTTCTCTCACTTGCCTGGAAAAGTGCAAGGCAAGAACCTGAGAAACGAGCCTGTTATGCAGACCCAAATCATCCTTGCGATGGGC

Variant names:

• chr15-51686717-T-TTGTTCAACTGCAACTGGCTGGTGGACTTGGAACTTTTTTTTCTCTCACTTGCCTGGAAAAGTGCAAGGCAAGAACCTGAGAAACGAGCCTGTTATGCAGACCCAAATCATCCTTGCGATGGGC
• NM_013243.4:c.398-1539_398-1538insCAACTGCAACTGGCTGGTGGACTTGGAACTTTTTTTTCTCTCACTTGCCTGGAAAAGTGCAAGGCAAGAACCTGAGAAACGAGCCTGTTATGCAGACCCAAATCATCCTTGCGATGGGCTGTT

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
• Clinical Significance: Uncertain significance no assertion criteria provided U:1
• 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]

ACMG classification

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 rank	MANE	Protein	UniProt
SCG3	NM_013243.4	c.398-1539_398-1538insCAACTGCAACTGGCTGGTGGACTTGGAACTTTTTTTTCTCTCACTTGCCTGGAAAAGTGCAAGGCAAGAACCTGAGAAACGAGCCTGTTATGCAGACCCAAATCATCCTTGCGATGGGCTGTT		intron_variant	Intron 4 of 11	ENST00000220478.8	NP_037375.2
SCG3	NM_001165257.2	c.-299-1539_-299-1538insCAACTGCAACTGGCTGGTGGACTTGGAACTTTTTTTTCTCTCACTTGCCTGGAAAAGTGCAAGGCAAGAACCTGAGAAACGAGCCTGTTATGCAGACCCAAATCATCCTTGCGATGGGCTGTT		intron_variant	Intron 3 of 10		NP_001158729.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCG3	ENST00000220478.8	c.398-1543_398-1542insTGTTCAACTGCAACTGGCTGGTGGACTTGGAACTTTTTTTTCTCTCACTTGCCTGGAAAAGTGCAAGGCAAGAACCTGAGAAACGAGCCTGTTATGCAGACCCAAATCATCCTTGCGATGGGC		intron_variant	Intron 4 of 11	1	NM_013243.4	ENSP00000220478.3
SCG3	ENST00000542355.6	c.-299-1543_-299-1542insTGTTCAACTGCAACTGGCTGGTGGACTTGGAACTTTTTTTTCTCTCACTTGCCTGGAAAAGTGCAAGGCAAGAACCTGAGAAACGAGCCTGTTATGCAGACCCAAATCATCCTTGCGATGGGC		intron_variant	Intron 3 of 10	2		ENSP00000445205.2
SCG3	ENST00000558709.1	c.-156-2502_-156-2501insTGTTCAACTGCAACTGGCTGGTGGACTTGGAACTTTTTTTTCTCTCACTTGCCTGGAAAAGTGCAAGGCAAGAACCTGAGAAACGAGCCTGTTATGCAGACCCAAATCATCCTTGCGATGGGC		intron_variant	Intron 3 of 4	2		ENSP00000452745.1

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: no assertion criteria provided

Submissions by phenotype

Schizophrenia Uncertain:1

Nov 11, 2022

Department of Psychiatry, The University of Hong Kong

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: case-control

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr15-51978914;