11-45283644-C-T

Position:

• chr11-45283644-C-T

Variant summary

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

The NM_020826.3(SYT13):​c.183+2381G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 152,128 control chromosomes in the GnomAD database, including 28,749 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 0.60 (28749 hom., cov: 33)
• Consequence: SYT13 NM_020826.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.784

Genes affected

SYT13 (HGNC:14962): (synaptotagmin 13) This gene encodes a member of the large synaptotagmin protein family. Family members have an extracellular N-terminal transmembrane domain and a cytoplasmic C terminus with two tandem C2 domains (C2A and C2B). Synaptotogmin family members can form homo- and heteromeric complexes with each other. They also have different biochemical properties and developmental profiles, and patterns of tissue distribution. Synaptotagmins function as membrane traffickers in multicellular organisms. Two alternatively spliced transcript variants that encode different protein isoforms have been described for this gene. [provided by RefSeq, Oct 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SYT13	NM_020826.3	c.183+2381G>A		intron_variant		ENST00000020926.8
SYT13	NM_001247987.2	c.-468+2381G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SYT13	ENST00000020926.8	c.183+2381G>A		intron_variant		1	NM_020826.3	P1
SYT13	ENST00000533332.1	c.43+2381G>A		intron_variant, NMD_transcript_variant		1
SYT13	ENST00000528101.1	c.62+2219G>A		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91631 AN: 152010 Hom.: 28734 Cov.: 33

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.603 AC: 91680 AN: 152128 Hom.: 28749 Cov.: 33 AF XY: 0.605 AC XY: 44949 AN XY: 74342

Gnomad4 AFR AF: 0.417

Gnomad4 AMR AF: 0.711

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.740

Gnomad4 SAS AF: 0.575

Gnomad4 FIN AF: 0.638

Gnomad4 NFE AF: 0.675

Gnomad4 OTH AF: 0.600

Alfa AF: 0.647 Hom.: 6592

Bravo AF: 0.605

Asia WGS AF: 0.602 AC: 2094 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	13
DANN	Benign	0.63

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: rs2289448; hg19: chr11-45305195;