rs2129209

Variant names:

• chr6-158734966-A-C
• rs2129209
• NM_001242394.2:c.855+9329A>C

Your query was ambiguous. Multiple possible variants found:

• chr6-158734966-A-C
• chr6-158734966-A-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.855+9329A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,090 control chromosomes in the GnomAD database, including 4,444 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 0.23 (4444 hom., cov: 32)
• Consequence: SYTL3 NM_001242394.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.816
• Publications: 13 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.396 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SYTL3	NM_001242394.2	MANE Select	c.855+9329A>C		intron	N/A	NP_001229323.1	Q4VX76-1
	SYTL3	NM_001242384.2		c.855+9329A>C		intron	N/A	NP_001229313.1	Q4VX76-1
	SYTL3	NM_001009991.4		c.651+9329A>C		intron	N/A	NP_001009991.2	Q4VX76-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SYTL3	ENST00000611299.5	TSL:5 MANE Select	c.855+9329A>C		intron	N/A	ENSP00000483936.1	Q4VX76-1
	SYTL3	ENST00000945463.1		c.1032+9329A>C		intron	N/A	ENSP00000615522.1
	SYTL3	ENST00000945466.1		c.966+9329A>C		intron	N/A	ENSP00000615525.1

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35646 AN: 151972 Hom.: 4434 Cov.: 32

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.235 AC: 35681 AN: 152090 Hom.: 4444 Cov.: 32 AF XY: 0.238 AC XY: 17666 AN XY: 74352

African (AFR) AF: 0.305 AC: 12626 AN: 41452

American (AMR) AF: 0.194 AC: 2964 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 480 AN: 3472

East Asian (EAS) AF: 0.164 AC: 848 AN: 5184

South Asian (SAS) AF: 0.411 AC: 1980 AN: 4812

European-Finnish (FIN) AF: 0.231 AC: 2450 AN: 10590

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13551 AN: 67982

Other (OTH) AF: 0.202 AC: 427 AN: 2114

Alfa AF: 0.204 Hom.: 14574

Bravo AF: 0.228

Asia WGS AF: 0.309 AC: 1072 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.1
DANN	Benign	0.29
PhyloP100		0.82
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: rs2129209; hg19: chr6-159155998;