11-7345864-T-C

Position:

• chr11-7345864-T-C

Variant summary

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

The NM_175733.4(SYT9):​c.1044+31923T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,192 control chromosomes in the GnomAD database, including 5,066 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 0.24 (5066 hom., cov: 33)
• Consequence: SYT9 NM_175733.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.244

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=-0.6).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SYT9	NM_175733.4	c.1044+31923T>C		intron_variant		ENST00000318881.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SYT9	ENST00000318881.11	c.1044+31923T>C		intron_variant		1	NM_175733.4	P1
SYT9	ENST00000524820.6	c.*141+31527T>C		intron_variant, NMD_transcript_variant		2
SYT9	ENST00000532592.1	c.497+42474T>C		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37117 AN: 152074 Hom.: 5067 Cov.: 33

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.0605

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.244 AC: 37131 AN: 152192 Hom.: 5066 Cov.: 33 AF XY: 0.242 AC XY: 18000 AN XY: 74410

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.264

Gnomad4 EAS AF: 0.0606

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.233

Alfa AF: 0.290 Hom.: 12410

Bravo AF: 0.229

Asia WGS AF: 0.128 AC: 446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	12
DANN	Benign	0.94

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: rs10769780; hg19: chr11-7367095;