rs724307

Variant names:

• chr16-19254659-C-A
• rs724307
• NM_016524.4:c.1229-12221C>A

Your query was ambiguous. Multiple possible variants found:

• chr16-19254659-C-A
• chr16-19254659-C-G
• chr16-19254659-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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=-0.88).
• 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 rank	MANE	Protein	UniProt
SYT17	NM_016524.4	c.1229-12221C>A		intron_variant	Intron 7 of 7	ENST00000355377.7	NP_057608.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SYT17	ENST00000355377.7	c.1229-12221C>A		intron_variant	Intron 7 of 7	1	NM_016524.4	ENSP00000347538.2
SYT17	ENST00000562034.5	c.1046-12221C>A		intron_variant	Intron 5 of 5	1		ENSP00000456252.1
SYT17	ENST00000562711.6	c.1217-12221C>A		intron_variant	Intron 7 of 7	2		ENSP00000454721.2
SYT17	ENST00000568433.1	c.311-12221C>A		intron_variant	Intron 3 of 3	3		ENSP00000456915.1

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

African (AFR) AF: 0.325 AC: 13453 AN: 41428

American (AMR) AF: 0.484 AC: 7391 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2193 AN: 3468

East Asian (EAS) AF: 0.633 AC: 3268 AN: 5166

South Asian (SAS) AF: 0.636 AC: 3055 AN: 4804

European-Finnish (FIN) AF: 0.598 AC: 6325 AN: 10572

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.611 AC: 41534 AN: 67954

Other (OTH) AF: 0.522 AC: 1101 AN: 2110

Alfa AF: 0.569 Hom.: 69411

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
PhyloP100		-1.2
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: rs724307; hg19: chr16-19265981;