16-30992641-C-CG

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_052874.5(STX1B):c.*179_*180insC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.038 (243 hom., cov: 0)
  • Exomes 𝑓: 0.040 (6 hom.)
• Consequence: STX1B NM_052874.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.551

Genes affected

STX1B (HGNC:18539): (syntaxin 1B) The protein encoded by this gene belongs to a family of proteins thought to play a role in the exocytosis of synaptic vesicles. Vesicle exocytosis releases vesicular contents and is important to various cellular functions. For instance, the secretion of transmitters from neurons plays an important role in synaptic transmission. After exocytosis, the membrane and proteins from the vesicle are retrieved from the plasma membrane through the process of endocytosis. Mutations in this gene have been identified as one cause of fever-associated epilepsy syndromes. A possible link between this gene and Parkinson's disease has also been suggested. [provided by RefSeq, Jan 2015]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 16-30992641-C-CG is Benign according to our data. Variant chr16-30992641-C-CG is described in ClinVar as [Benign]. Clinvar id is 1267591.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STX1B	NM_052874.5	c.*179_*180insC		3_prime_UTR_variant	10/10	ENST00000215095.11
STX1B	XM_017022893.2	c.*179_*180insC		3_prime_UTR_variant	10/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STX1B	ENST00000215095.11	c.*179_*180insC		3_prime_UTR_variant	10/10	1	NM_052874.5	P1

Frequencies

GnomAD3 genomes AF: 0.0378 AC: 3790 AN: 100238 Hom.: 240 Cov.: 0

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.0129

Gnomad AMR AF: 0.0165

Gnomad ASJ AF: 0.0213

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00193

Gnomad FIN AF: 0.00407

Gnomad MID AF: 0.00510

Gnomad NFE AF: 0.00296

Gnomad OTH AF: 0.0265

GnomAD4 exome AF: 0.0397 AC: 12008 AN: 302400 Hom.: 6 Cov.: 0 AF XY: 0.0387 AC XY: 6091 AN XY: 157352

Gnomad4 AFR exome AF: 0.165

Gnomad4 AMR exome AF: 0.0370

Gnomad4 ASJ exome AF: 0.0424

Gnomad4 EAS exome AF: 0.000610

Gnomad4 SAS exome AF: 0.0282

Gnomad4 FIN exome AF: 0.0352

Gnomad4 NFE exome AF: 0.0395

Gnomad4 OTH exome AF: 0.0497

GnomAD4 genome AF: 0.0379 AC: 3797 AN: 100282 Hom.: 243 Cov.: 0 AF XY: 0.0379 AC XY: 1779 AN XY: 46898

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.0163

Gnomad4 ASJ AF: 0.0213

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00195

Gnomad4 FIN AF: 0.00407

Gnomad4 NFE AF: 0.00296

Gnomad4 OTH AF: 0.0261

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 08, 2019

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs56353515; hg19: chr16-31003962;