1-155859720-C-T

Variant names:

• chr1-155859720-C-T
• rs3820594
• NM_152280.5:c.-42C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 26 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152280.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SYT11	NM_152280.5	MANE Select	c.-42C>T		5_prime_UTR	Exon 1 of 4	NP_689493.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SYT11	ENST00000368324.5	TSL:1 MANE Select	c.-42C>T		5_prime_UTR	Exon 1 of 4	ENSP00000357307.4	Q9BT88
	SYT11	ENST00000874873.1		c.-42C>T		5_prime_UTR	Exon 1 of 4	ENSP00000544932.1
	SYT11	ENST00000916078.1		c.-42C>T		5_prime_UTR	Exon 1 of 4	ENSP00000586137.1

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

GnomAD2 exomes AF: 0.337 AC: 84714 AN: 251350 AF XY: 0.331

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 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

African (AFR) AF: 0.176 AC: 5847 AN: 33310

American (AMR) AF: 0.442 AC: 19745 AN: 44704

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 6553 AN: 26076

East Asian (EAS) AF: 0.743 AC: 29452 AN: 39664

South Asian (SAS) AF: 0.333 AC: 28656 AN: 86078

European-Finnish (FIN) AF: 0.307 AC: 16361 AN: 53356

Middle Eastern (MID) AF: 0.209 AC: 1198 AN: 5742

European-Non Finnish (NFE) AF: 0.287 AC: 316601 AN: 1104852

Other (OTH) AF: 0.303 AC: 18201 AN: 60130

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

African (AFR) AF: 0.181 AC: 7512 AN: 41534

American (AMR) AF: 0.324 AC: 4964 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 842 AN: 3470

East Asian (EAS) AF: 0.702 AC: 3624 AN: 5162

South Asian (SAS) AF: 0.339 AC: 1637 AN: 4824

European-Finnish (FIN) AF: 0.313 AC: 3309 AN: 10576

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19508 AN: 67976

Other (OTH) AF: 0.284 AC: 602 AN: 2116

Alfa AF: 0.281 Hom.: 8305

Bravo AF: 0.280

Asia WGS AF: 0.508 AC: 1766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	14
DANN	Benign	0.85
PhyloP100		1.2
PromoterAI		-0.071	Neutral
Mutation Taster		=298/2	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3820594; hg19: chr1-155829511;