rs7188617

Variant names:

• chr16-19198774-G-A
• rs7188617
• NM_016524.4:c.951+14627G>A

Variant summary

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

The NM_016524.4(SYT17):​c.951+14627G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,200 control chromosomes in the GnomAD database, including 2,490 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 0.18 (2490 hom., cov: 33)
• Consequence: SYT17 NM_016524.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SYT17	NM_016524.4	c.951+14627G>A		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+14627G>A		intron_variant	Intron 5 of 7	1	NM_016524.4	ENSP00000347538.2

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26682 AN: 152082 Hom.: 2488 Cov.: 33

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.175 AC: 26689 AN: 152200 Hom.: 2490 Cov.: 33 AF XY: 0.175 AC XY: 13013 AN XY: 74410

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.151

Alfa AF: 0.147 Hom.: 3297

Bravo AF: 0.184

Asia WGS AF: 0.149 AC: 521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.76
DANN	Benign	0.47

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: rs7188617; hg19: chr16-19210096;