6-158684381-T-G

Variant names:

• chr6-158684381-T-G
• rs1979541
• NM_001242394.2:c.394+1392T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001242394.2(SYTL3):​c.394+1392T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,208 control chromosomes in the GnomAD database, including 9,460 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 0.27 (9460 hom., cov: 32)
• Consequence: SYTL3 NM_001242394.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 7 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001242394.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SYTL3	NM_001242394.2	MANE Select	c.394+1392T>G		intron	N/A	NP_001229323.1
	SYTL3	NM_001242384.2		c.394+1392T>G		intron	N/A	NP_001229313.1
	SYTL3	NM_001009991.4		c.394+1392T>G		intron	N/A	NP_001009991.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SYTL3	ENST00000611299.5	TSL:5 MANE Select	c.394+1392T>G		intron	N/A	ENSP00000483936.1
	SYTL3	ENST00000360448.8	TSL:5	c.394+1392T>G		intron	N/A	ENSP00000353631.4
	SYTL3	ENST00000367081.7	TSL:5	c.394+1392T>G		intron	N/A	ENSP00000356048.4

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40294 AN: 152090 Hom.: 9414 Cov.: 32

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.0798

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.0791

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.265 AC: 40387 AN: 152208 Hom.: 9460 Cov.: 32 AF XY: 0.259 AC XY: 19262 AN XY: 74430

African (AFR) AF: 0.637 AC: 26422 AN: 41502

American (AMR) AF: 0.163 AC: 2491 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 664 AN: 3472

East Asian (EAS) AF: 0.0798 AC: 413 AN: 5178

South Asian (SAS) AF: 0.215 AC: 1037 AN: 4832

European-Finnish (FIN) AF: 0.0791 AC: 840 AN: 10614

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7775 AN: 68000

Other (OTH) AF: 0.266 AC: 561 AN: 2110

Alfa AF: 0.128 Hom.: 1072

Bravo AF: 0.287

Asia WGS AF: 0.186 AC: 643 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.028
DANN	Benign	0.46
PhyloP100		-1.3
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: rs1979541; hg19: chr6-159105413;