rs2387137

Positions:

• chr19-50634403-C-T

Variant summary

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

The NM_001160329.2(SYT3):​c.149-1592G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.817 in 152,142 control chromosomes in the GnomAD database, including 51,900 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 0.82 (51900 hom., cov: 30)
• Consequence: SYT3 NM_001160329.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.475

Genes affected

SYT3 (HGNC:11511): (synaptotagmin 3) Predicted to enable several functions, including phospholipid binding activity; protein dimerization activity; and syntaxin binding activity. Involved in positive regulation of dendrite extension. Located in endosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SYT3	NM_001160329.2	c.149-1592G>A		intron_variant		ENST00000600079.6
SYT3	NM_001160328.2	c.149-1592G>A		intron_variant
SYT3	NM_032298.3	c.149-1592G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SYT3	ENST00000600079.6	c.149-1592G>A		intron_variant		1	NM_001160329.2	P1
SYT3	ENST00000338916.8	c.149-1592G>A		intron_variant		1		P1
SYT3	ENST00000593901.5	c.149-1592G>A		intron_variant		1		P1
SYT3	ENST00000598997.1	c.149-1592G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.817 AC: 124168 AN: 152024 Hom.: 51869 Cov.: 30

Gnomad AFR AF: 0.906

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.877

Gnomad MID AF: 0.787

Gnomad NFE AF: 0.824

Gnomad OTH AF: 0.795

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

GnomAD4 genome AF: 0.817 AC: 124245 AN: 152142 Hom.: 51900 Cov.: 30 AF XY: 0.812 AC XY: 60409 AN XY: 74350

Gnomad4 AFR AF: 0.905

Gnomad4 AMR AF: 0.763

Gnomad4 ASJ AF: 0.770

Gnomad4 EAS AF: 0.257

Gnomad4 SAS AF: 0.640

Gnomad4 FIN AF: 0.877

Gnomad4 NFE AF: 0.824

Gnomad4 OTH AF: 0.789

Alfa AF: 0.813 Hom.: 40741

Bravo AF: 0.812

Asia WGS AF: 0.535 AC: 1863 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
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: rs2387137; hg19: chr19-51137660;