16-30992641-CG-C

Variant summary

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

The NM_052874.5(STX1B):c.*179del 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 0.76 (29376 hom., cov: 0)
  • Exomes 𝑓: 0.75 (85800 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-CG-C is Benign according to our data. Variant chr16-30992641-CG-C is described in ClinVar as [Benign]. Clinvar id is 1267927.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.944 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.761 AC: 76456 AN: 100434 Hom.: 29368 Cov.: 0

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.766

Gnomad AMR AF: 0.843

Gnomad ASJ AF: 0.807

Gnomad EAS AF: 0.969

Gnomad SAS AF: 0.925

Gnomad FIN AF: 0.850

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.812

Gnomad OTH AF: 0.786

GnomAD4 exome AF: 0.754 AC: 232670 AN: 308642 Hom.: 85800 Cov.: 0 AF XY: 0.757 AC XY: 121605 AN XY: 160618

Gnomad4 AFR exome AF: 0.432

Gnomad4 AMR exome AF: 0.779

Gnomad4 ASJ exome AF: 0.752

Gnomad4 EAS exome AF: 0.925

Gnomad4 SAS exome AF: 0.826

Gnomad4 FIN exome AF: 0.766

Gnomad4 NFE exome AF: 0.738

Gnomad4 OTH exome AF: 0.728

GnomAD4 genome AF: 0.761 AC: 76486 AN: 100482 Hom.: 29376 Cov.: 0 AF XY: 0.767 AC XY: 36065 AN XY: 47000

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.843

Gnomad4 ASJ AF: 0.807

Gnomad4 EAS AF: 0.970

Gnomad4 SAS AF: 0.924

Gnomad4 FIN AF: 0.850

Gnomad4 NFE AF: 0.812

Gnomad4 OTH AF: 0.789

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 15, 2019

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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;