11-7355074-A-G

Position:

• chr11-7355074-A-G

Variant summary

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

The NM_175733.4(SYT9):​c.1044+41133A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 152,162 control chromosomes in the GnomAD database, including 6,559 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 0.28 (6559 hom., cov: 32)
• Consequence: SYT9 NM_175733.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.538

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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SYT9	NM_175733.4	c.1044+41133A>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.1044+41133A>G		intron_variant		1	NM_175733.4	ENSP00000324419.6
SYT9	ENST00000524820.6	n.*141+40737A>G		intron_variant		2		ENSP00000432141.2
SYT9	ENST00000532592.1	n.497+51684A>G		intron_variant		2		ENSP00000434558.1

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42089 AN: 152044 Hom.: 6561 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.277 AC: 42082 AN: 152162 Hom.: 6559 Cov.: 32 AF XY: 0.273 AC XY: 20291 AN XY: 74374

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.358

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.250

Alfa AF: 0.313 Hom.: 2449

Bravo AF: 0.266

Asia WGS AF: 0.205 AC: 714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.9
DANN	Benign	0.68

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: rs991697; hg19: chr11-7376305;