rs229018

chr16-19211391-T-G

Variant summary

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

The NM_016524.4(SYT17):c.952-11654T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 703,124 control chromosomes in the GnomAD database, including 22,324 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 (6273 hom., cov: 31)
  • Exomes 𝑓: 0.23 (16051 hom.)
• Consequence: SYT17 NM_016524.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.647

Genes affected

SYT17 (HGNC:24119): (synaptotagmin 17) Predicted to enable several functions, including calcium ion binding activity; phospholipid binding activity; and syntaxin binding activity. Involved in positive regulation of dendrite extension. Predicted to be located in trans-Golgi network. Predicted to be active in exocytic vesicle and plasma 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SYT17	NM_016524.4	c.952-11654T>G		intron_variant		ENST00000355377.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SYT17	ENST00000355377.7	c.952-11654T>G		intron_variant		1	NM_016524.4	P1

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42009 AN: 151822 Hom.: 6264 Cov.: 31

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.249

GnomAD3 exomes AF: 0.227 AC: 31049 AN: 136930 Hom.: 3848 AF XY: 0.223 AC XY: 16436 AN XY: 73546

Gnomad AFR exome AF: 0.377

Gnomad AMR exome AF: 0.191

Gnomad ASJ exome AF: 0.305

Gnomad EAS exome AF: 0.112

Gnomad SAS exome AF: 0.164

Gnomad FIN exome AF: 0.236

Gnomad NFE exome AF: 0.258

Gnomad OTH exome AF: 0.230

GnomAD4 exome AF: 0.232 AC: 128111 AN: 551184 Hom.: 16051 Cov.: 0 AF XY: 0.228 AC XY: 68062 AN XY: 298358

Gnomad4 AFR exome AF: 0.381

Gnomad4 AMR exome AF: 0.194

Gnomad4 ASJ exome AF: 0.306

Gnomad4 EAS exome AF: 0.0889

Gnomad4 SAS exome AF: 0.171

Gnomad4 FIN exome AF: 0.222

Gnomad4 NFE exome AF: 0.252

Gnomad4 OTH exome AF: 0.244

GnomAD4 genome AF: 0.277 AC: 42051 AN: 151940 Hom.: 6273 Cov.: 31 AF XY: 0.272 AC XY: 20241 AN XY: 74300

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.297

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.228

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.247

Alfa AF: 0.255 Hom.: 3076

Bravo AF: 0.283

Asia WGS AF: 0.145 AC: 503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.8
Dann	Benign	0.42

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: rs229018; hg19: chr16-19222713;