rs9456350

Variant names:

• chr6-158746253-A-G
• rs9456350
• NM_001242394.2:c.1034+595A>G

Variant summary

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

The NM_001242394.2(SYTL3):​c.1034+595A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.542 in 151,432 control chromosomes in the GnomAD database, including 23,113 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 0.54 (23113 hom., cov: 28)
• Consequence: SYTL3 NM_001242394.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SYTL3	NM_001242394.2	c.1034+595A>G		intron_variant	Intron 12 of 17	ENST00000611299.5	NP_001229323.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SYTL3	ENST00000611299.5	c.1034+595A>G		intron_variant	Intron 12 of 17	5	NM_001242394.2	ENSP00000483936.1
SYTL3	ENST00000360448.8	c.1034+595A>G		intron_variant	Intron 13 of 18	5		ENSP00000353631.4
SYTL3	ENST00000367081.7	c.830+595A>G		intron_variant	Intron 10 of 15	5		ENSP00000356048.4

Frequencies

GnomAD3 genomes AF: 0.542 AC: 81958 AN: 151314 Hom.: 23107 Cov.: 28

Gnomad AFR AF: 0.610

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.542 AC: 82002 AN: 151432 Hom.: 23113 Cov.: 28 AF XY: 0.539 AC XY: 39832 AN XY: 73958

Gnomad4 AFR AF: 0.610

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.536

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.656

Gnomad4 NFE AF: 0.556

Gnomad4 OTH AF: 0.519

Alfa AF: 0.543 Hom.: 6656

Bravo AF: 0.519

Asia WGS AF: 0.311 AC: 1083 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.66
DANN	Benign	0.37

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: rs9456350; hg19: chr6-159167285;