rs4351800
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_175733.4(SYT9):c.*1788A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 340,782 control chromosomes in the GnomAD database, including 58,956 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 0.60 ( 27718 hom., cov: 33)
Exomes 𝑓: 0.57 ( 31238 hom. )
Consequence
SYT9
NM_175733.4 3_prime_UTR
NM_175733.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.15
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=-0.82).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SYT9 | NM_175733.4 | c.*1788A>C | 3_prime_UTR_variant | 7/7 | ENST00000318881.11 | ||
SYT9 | XM_011519901.3 | c.*1720A>C | 3_prime_UTR_variant | 8/8 | |||
SYT9 | XM_047426379.1 | c.*1788A>C | 3_prime_UTR_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYT9 | ENST00000318881.11 | c.*1788A>C | 3_prime_UTR_variant | 7/7 | 1 | NM_175733.4 | P1 | ||
SYT9-AS1 | ENST00000530201.2 | n.1351-18146T>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.599 AC: 91055AN: 152004Hom.: 27673 Cov.: 33
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GnomAD4 exome AF: 0.570 AC: 107541AN: 188658Hom.: 31238 Cov.: 0 AF XY: 0.570 AC XY: 54545AN XY: 95768
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GnomAD4 genome ? AF: 0.599 AC: 91161AN: 152124Hom.: 27718 Cov.: 33 AF XY: 0.601 AC XY: 44657AN XY: 74352
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at