rs10489346

chr1-210061963-A-G

Variant summary

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

The NM_001146262.4(SYT14):c.443-32359A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.05 in 151,740 control chromosomes in the GnomAD database, including 1,038 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 0.050 (1038 hom., cov: 32)
• Consequence: SYT14 NM_001146262.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.489

Genes affected

SYT14 (HGNC:23143): (synaptotagmin 14) This gene is a member of the synaptotagmin gene family and encodes a protein similar to other family members that mediate membrane trafficking in synaptic transmission. The encoded protein is a calcium-independent synaptotagmin. Mutations in this gene are a cause of autosomal recessive spinocerebellar ataxia-11 (SCAR11), and a t(1;3) translocation of this gene has been associated with neurodevelopmental abnormalities. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the long arm of chromosome 4. [provided by RefSeq, Dec 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SYT14	NM_001146262.4	c.443-32359A>G		intron_variant		ENST00000367019.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SYT14	ENST00000367019.6	c.443-32359A>G		intron_variant		1	NM_001146262.4

Frequencies

GnomAD3 genomes AF: 0.0500 AC: 7583 AN: 151622 Hom.: 1035 Cov.: 32

Gnomad AFR AF: 0.00906

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.0205

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.0985

Gnomad FIN AF: 0.0179

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00956

Gnomad OTH AF: 0.0537

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

GnomAD4 genome AF: 0.0500 AC: 7592 AN: 151740 Hom.: 1038 Cov.: 32 AF XY: 0.0574 AC XY: 4259 AN XY: 74148

Gnomad4 AFR AF: 0.00904

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.0205

Gnomad4 EAS AF: 0.419

Gnomad4 SAS AF: 0.0982

Gnomad4 FIN AF: 0.0179

Gnomad4 NFE AF: 0.00956

Gnomad4 OTH AF: 0.0536

Alfa AF: 0.0259 Hom.: 41

Bravo AF: 0.0693

Asia WGS AF: 0.216 AC: 753 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	6.8
Dann	Benign	0.68

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: rs10489346; hg19: chr1-210235308;