11-45240575-C-T

Position:

• chr11-45240575-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.*3477G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 152,032 control chromosomes in the GnomAD database, including 16,789 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 0.46 (16787 hom., cov: 33)
  • Exomes 𝑓: 0.56 (2 hom.)
• Consequence: SYT13 NM_020826.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420

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 (NFE) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SYT13	NM_020826.3	c.*3477G>A		3_prime_UTR_variant	6/6	ENST00000020926.8	NP_065877.1
SYT13	NM_001247987.2	c.*3477G>A		3_prime_UTR_variant	8/8		NP_001234916.1
SYT13	XM_047427338.1	c.*3477G>A		3_prime_UTR_variant	6/6		XP_047283294.1
SYT13	XM_047427339.1	c.*3477G>A		3_prime_UTR_variant	6/6		XP_047283295.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SYT13	ENST00000020926.8	c.*3477G>A		3_prime_UTR_variant	6/6	1	NM_020826.3	ENSP00000020926	P1

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70316 AN: 151896 Hom.: 16783 Cov.: 33

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.502

GnomAD4 exome AF: 0.556 AC: 10 AN: 18 Hom.: 2 Cov.: 0 AF XY: 0.600 AC XY: 6 AN XY: 10

Gnomad4 FIN exome AF: 0.625

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.463 AC: 70341 AN: 152014 Hom.: 16787 Cov.: 33 AF XY: 0.457 AC XY: 33958 AN XY: 74288

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.528

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.504

Gnomad4 NFE AF: 0.530

Gnomad4 OTH AF: 0.507

Alfa AF: 0.520 Hom.: 35048

Bravo AF: 0.449

Asia WGS AF: 0.407 AC: 1415 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	1.3
DANN	Benign	0.72

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: rs8929; hg19: chr11-45262126; COSMIC: COSV50073789; COSMIC: COSV50073789;