rs9364496

chr6-158701052-G-Achr6-158701052-G-Cchr6-158701052-G-T

Variant summary

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

The NM_001242394.2(SYTL3):c.395-6178G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,154 control chromosomes in the GnomAD database, including 7,249 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 0.29 (7249 hom., cov: 32)
• Consequence: SYTL3 NM_001242394.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250

Genes affected

SYTL3 (HGNC:15587): (synaptotagmin like 3) The protein encoded by this gene belongs to a family of peripheral membrane proteins that play a role in vesicular trafficking. This protein binds phospholipids in the presence of calcium ions. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.777 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SYTL3	NM_001242394.2	c.395-6178G>A		intron_variant		ENST00000611299.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SYTL3	ENST00000611299.5	c.395-6178G>A		intron_variant		5	NM_001242394.2	P1
SYTL3	ENST00000360448.8	c.395-6178G>A		intron_variant		5		P1
SYTL3	ENST00000367081.7	c.395-6178G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43436 AN: 152036 Hom.: 7232 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.286 AC: 43467 AN: 152154 Hom.: 7249 Cov.: 32 AF XY: 0.294 AC XY: 21876 AN XY: 74396

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.419

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.797

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.283

Alfa AF: 0.275 Hom.: 8168

Bravo AF: 0.295

Asia WGS AF: 0.517 AC: 1795 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	4.7
Dann	Benign	0.72

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: rs9364496; hg19: chr6-159122084;