chr6-158762530-T-C

Variant names:

• chr6-158762530-T-C
• rs2171209
• NM_001242394.2:c.1517+352T>C

Variant summary

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

The NM_001242394.2(SYTL3):​c.1517+352T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.764 in 152,068 control chromosomes in the GnomAD database, including 46,059 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 0.76 (46059 hom., cov: 31)
• Consequence: SYTL3 NM_001242394.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27
• Publications: 16 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.851 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.1517+352T>C		intron	N/A	NP_001229323.1
	SYTL3	NM_001242384.2		c.1517+352T>C		intron	N/A	NP_001229313.1
	SYTL3	NM_001009991.4		c.1313+352T>C		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.1517+352T>C		intron	N/A	ENSP00000483936.1
	SYTL3	ENST00000360448.8	TSL:5	c.1517+352T>C		intron	N/A	ENSP00000353631.4
	SYTL3	ENST00000367081.7	TSL:5	c.1313+352T>C		intron	N/A	ENSP00000356048.4

Frequencies

GnomAD3 genomes AF: 0.764 AC: 116103 AN: 151950 Hom.: 46002 Cov.: 31

Gnomad AFR AF: 0.858

Gnomad AMI AF: 0.932

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.885

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.764 AC: 116224 AN: 152068 Hom.: 46059 Cov.: 31 AF XY: 0.759 AC XY: 56437 AN XY: 74314

African (AFR) AF: 0.858 AC: 35582 AN: 41464

American (AMR) AF: 0.542 AC: 8268 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2455 AN: 3468

East Asian (EAS) AF: 0.191 AC: 986 AN: 5166

South Asian (SAS) AF: 0.658 AC: 3170 AN: 4818

European-Finnish (FIN) AF: 0.885 AC: 9371 AN: 10594

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.792 AC: 53849 AN: 67994

Other (OTH) AF: 0.712 AC: 1506 AN: 2114

Alfa AF: 0.759 Hom.: 75547

Bravo AF: 0.735

Asia WGS AF: 0.488 AC: 1697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.50
DANN	Benign	0.55
PhyloP100		-2.3
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: rs2171209; hg19: chr6-159183562;