rs9932538

Variant names:

• chr16-19197247-A-G
• rs9932538
• NM_016524.4:c.951+13100A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016524.4(SYT17):​c.951+13100A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,226 control chromosomes in the GnomAD database, including 2,140 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 0.16 (2140 hom., cov: 33)
• Consequence: SYT17 NM_016524.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.314
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SYT17	NM_016524.4	c.951+13100A>G		intron_variant	Intron 5 of 7	ENST00000355377.7	NP_057608.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SYT17	ENST00000355377.7	c.951+13100A>G		intron_variant	Intron 5 of 7	1	NM_016524.4	ENSP00000347538.2

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24730 AN: 152108 Hom.: 2136 Cov.: 33

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.0186

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.163 AC: 24753 AN: 152226 Hom.: 2140 Cov.: 33 AF XY: 0.160 AC XY: 11880 AN XY: 74438

African (AFR) AF: 0.202 AC: 8405 AN: 41516

American (AMR) AF: 0.156 AC: 2386 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 725 AN: 3464

East Asian (EAS) AF: 0.0187 AC: 97 AN: 5190

South Asian (SAS) AF: 0.175 AC: 844 AN: 4830

European-Finnish (FIN) AF: 0.108 AC: 1142 AN: 10602

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10572 AN: 68004

Other (OTH) AF: 0.165 AC: 349 AN: 2112

Alfa AF: 0.156 Hom.: 4568

Bravo AF: 0.167

Asia WGS AF: 0.123 AC: 430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.55
PhyloP100		0.31
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9932538; hg19: chr16-19208569;