rs724307

chr16-19254659-C-Achr16-19254659-C-Gchr16-19254659-C-T

Variant summary

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

The NM_016524.4(SYT17):c.1229-12221C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 151,978 control chromosomes in the GnomAD database, including 21,833 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 0.52 (21833 hom., cov: 32)
• Consequence: SYT17 NM_016524.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

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]

LOC105371114 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SYT17	NM_016524.4	c.1229-12221C>A		intron_variant		ENST00000355377.7
LOC105371114	XR_001752097.2	n.724G>T		non_coding_transcript_exon_variant	4/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SYT17	ENST00000355377.7	c.1229-12221C>A		intron_variant		1	NM_016524.4	P1
SYT17	ENST00000562034.5	c.1046-12221C>A		intron_variant		1
SYT17	ENST00000562711.6	c.1217-12221C>A		intron_variant		2
SYT17	ENST00000568433.1	c.311-12221C>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78882 AN: 151860 Hom.: 21840 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.519 AC: 78895 AN: 151978 Hom.: 21833 Cov.: 32 AF XY: 0.522 AC XY: 38772 AN XY: 74286

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.633

Gnomad4 SAS AF: 0.636

Gnomad4 FIN AF: 0.598

Gnomad4 NFE AF: 0.611

Gnomad4 OTH AF: 0.522

Alfa AF: 0.589 Hom.: 43389

Bravo AF: 0.500

Asia WGS AF: 0.613 AC: 2132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.0
Dann	Benign	0.81

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: rs724307; hg19: chr16-19265981;