rs16924131
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_175733.4(SYT9):c.145+15143T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0229 in 151,664 control chromosomes in the GnomAD database, including 48 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.023 ( 48 hom., cov: 32)
Consequence
SYT9
NM_175733.4 intron
NM_175733.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.459
Genes affected
SYT9 (HGNC:19265): (synaptotagmin 9) Predicted to enable several functions, including calcium ion binding activity; phospholipid binding activity; and syntaxin binding activity. Predicted to be involved in calcium-ion regulated exocytosis; cellular response to calcium ion; and regulation of secretion by cell. Predicted to be located in clathrin-coated endocytic vesicle membrane. Predicted to be active in hippocampal mossy fiber to CA3 synapse; plasma membrane; and secretory vesicle. Predicted to be integral component of synaptic vesicle membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0229 (3471/151664) while in subpopulation AFR AF= 0.0406 (1682/41416). AF 95% confidence interval is 0.039. There are 48 homozygotes in gnomad4. There are 1648 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 48 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SYT9 | NM_175733.4 | c.145+15143T>C | intron_variant | ENST00000318881.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYT9 | ENST00000318881.11 | c.145+15143T>C | intron_variant | 1 | NM_175733.4 | P1 | |||
SYT9 | ENST00000524820.6 | c.49+28558T>C | intron_variant, NMD_transcript_variant | 2 | |||||
SYT9 | ENST00000532592.1 | c.145+15143T>C | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0229 AC: 3468AN: 151546Hom.: 48 Cov.: 32
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0229 AC: 3471AN: 151664Hom.: 48 Cov.: 32 AF XY: 0.0222 AC XY: 1648AN XY: 74076
GnomAD4 genome
?
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3471
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32
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1648
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74076
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19
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3464
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at