rs9364496

Variant names:

• chr6-158701052-G-A
• rs9364496
• NM_001242394.2:c.395-6178G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-158701052-G-A
• chr6-158701052-G-C
• chr6-158701052-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SYTL3	NM_001242394.2	c.395-6178G>A		intron_variant	Intron 6 of 17	ENST00000611299.5	NP_001229323.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SYTL3	ENST00000611299.5	c.395-6178G>A		intron_variant	Intron 6 of 17	5	NM_001242394.2	ENSP00000483936.1
SYTL3	ENST00000360448.8	c.395-6178G>A		intron_variant	Intron 7 of 18	5		ENSP00000353631.4
SYTL3	ENST00000367081.7	c.395-6178G>A		intron_variant	Intron 6 of 15	5		ENSP00000356048.4

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

African (AFR) AF: 0.195 AC: 8086 AN: 41524

American (AMR) AF: 0.419 AC: 6405 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 855 AN: 3470

East Asian (EAS) AF: 0.797 AC: 4126 AN: 5174

South Asian (SAS) AF: 0.335 AC: 1613 AN: 4822

European-Finnish (FIN) AF: 0.282 AC: 2980 AN: 10586

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18548 AN: 67982

Other (OTH) AF: 0.283 AC: 598 AN: 2114

Alfa AF: 0.275 Hom.: 9696

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
PhyloP100		0.025
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: rs9364496; hg19: chr6-159122084;