1-155859720-C-T

Position:

• chr1-155859720-C-T

Variant summary

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

The NM_152280.5(SYT11):​c.-42C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 1,606,072 control chromosomes in the GnomAD database, including 79,840 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 0.28 (6624 hom., cov: 33)
  • Exomes 𝑓: 0.30 (73216 hom.)
• Consequence: SYT11 NM_152280.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22

Genes affected

SYT11 (HGNC:19239): (synaptotagmin 11) This gene is a member of the synaptotagmin gene family and encodes a protein similar to other family members that are known calcium sensors and mediate calcium-dependent regulation of membrane trafficking in synaptic transmission. The encoded protein is also a substrate for ubiquitin-E3-ligase parkin. The gene has previously been referred to as synaptotagmin XII but has been renamed synaptotagmin XI to be consistent with mouse and rat official nomenclature. [provided by RefSeq, Apr 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SYT11	NM_152280.5	c.-42C>T		5_prime_UTR_variant	1/4	ENST00000368324.5
SYT11	XM_005245014.4	c.-42C>T		5_prime_UTR_variant	1/4
SYT11	XM_017000759.3	c.-42C>T		5_prime_UTR_variant	1/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SYT11	ENST00000368324.5	c.-42C>T		5_prime_UTR_variant	1/4	1	NM_152280.5	P1

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42217 AN: 152042 Hom.: 6615 Cov.: 33

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.702

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.287

GnomAD3 exomes AF: 0.337 AC: 84714 AN: 251350 Hom.: 16342 AF XY: 0.331 AC XY: 45030 AN XY: 135840

Gnomad AFR exome AF: 0.178

Gnomad AMR exome AF: 0.455

Gnomad ASJ exome AF: 0.254

Gnomad EAS exome AF: 0.697

Gnomad SAS exome AF: 0.338

Gnomad FIN exome AF: 0.314

Gnomad NFE exome AF: 0.278

Gnomad OTH exome AF: 0.311

GnomAD4 exome AF: 0.304 AC: 442614 AN: 1453912 Hom.: 73216 Cov.: 29 AF XY: 0.304 AC XY: 219854 AN XY: 723818

Gnomad4 AFR exome AF: 0.176

Gnomad4 AMR exome AF: 0.442

Gnomad4 ASJ exome AF: 0.251

Gnomad4 EAS exome AF: 0.743

Gnomad4 SAS exome AF: 0.333

Gnomad4 FIN exome AF: 0.307

Gnomad4 NFE exome AF: 0.287

Gnomad4 OTH exome AF: 0.303

GnomAD4 genome AF: 0.278 AC: 42243 AN: 152160 Hom.: 6624 Cov.: 33 AF XY: 0.282 AC XY: 20977 AN XY: 74382

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.702

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.284

Alfa AF: 0.282 Hom.: 6442

Bravo AF: 0.280

Asia WGS AF: 0.508 AC: 1766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	14
DANN	Benign	0.85

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: rs3820594; hg19: chr1-155829511;