rs10769783

Positions:

• chr11-7374960-A-G
• chr11-7374960-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_175733.4(SYT9):​c.1045-41082A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,106 control chromosomes in the GnomAD database, including 1,727 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 0.13 (1727 hom., cov: 32)
• Consequence: SYT9 NM_175733.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.77

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SYT9	NM_175733.4	c.1045-41082A>G		intron_variant		ENST00000318881.11	NP_783860.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SYT9	ENST00000318881.11	c.1045-41082A>G		intron_variant		1	NM_175733.4	ENSP00000324419	P1
SYT9	ENST00000524820.6	c.*142-41082A>G		intron_variant, NMD_transcript_variant		2		ENSP00000432141
SYT9	ENST00000532592.1	c.498-41082A>G		intron_variant, NMD_transcript_variant		2		ENSP00000434558

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19615 AN: 151988 Hom.: 1725 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.0630

Gnomad ASJ AF: 0.0791

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.0499

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0794

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.129 AC: 19629 AN: 152106 Hom.: 1727 Cov.: 32 AF XY: 0.129 AC XY: 9601 AN XY: 74366

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.0630

Gnomad4 ASJ AF: 0.0791

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.0495

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.0794

Gnomad4 OTH AF: 0.105

Alfa AF: 0.101 Hom.: 139

Bravo AF: 0.130

Asia WGS AF: 0.135 AC: 470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.22
DANN	Benign	0.25

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10769783; hg19: chr11-7396191;