16-30992811-T-TG

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_052874.5(STX1B):c.*9_*10insC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000888 in 1,162,518 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0021 (0 hom., cov: 30)
  • Exomes 𝑓: 0.00085 (2 hom.)
• Consequence: STX1B NM_052874.5 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.651

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 Likely_benign. Variant got -6 ACMG points.

• BP6: Variant 16-30992811-T-TG is Benign according to our data. Variant chr16-30992811-T-TG is described in ClinVar as [Likely_benign]. Clinvar id is 1219053.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomAd at 79 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STX1B	NM_052874.5	c.*9_*10insC		3_prime_UTR_variant	10/10	ENST00000215095.11
STX1B	XM_017022893.2	c.*9_*10insC		3_prime_UTR_variant	10/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STX1B	ENST00000215095.11	c.*9_*10insC		3_prime_UTR_variant	10/10	1	NM_052874.5	P1

Frequencies

GnomAD3 genomes AF: 0.00206 AC: 79 AN: 38418 Hom.: 0 Cov.: 30

Gnomad AFR AF: 0.000752

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000474

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00169

Gnomad FIN AF: 0.0112

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00212

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000848 AC: 953 AN: 1124022 Hom.: 2 Cov.: 29 AF XY: 0.000888 AC XY: 495 AN XY: 557274

Gnomad4 AFR exome AF: 0.000642

Gnomad4 AMR exome AF: 0.0000616

Gnomad4 ASJ exome AF: 0.000367

Gnomad4 EAS exome AF: 0.000322

Gnomad4 SAS exome AF: 0.000252

Gnomad4 FIN exome AF: 0.00714

Gnomad4 NFE exome AF: 0.000729

Gnomad4 OTH exome AF: 0.000760

GnomAD4 genome AF: 0.00205 AC: 79 AN: 38496 Hom.: 0 Cov.: 30 AF XY: 0.00207 AC XY: 40 AN XY: 19284

Gnomad4 AFR AF: 0.000748

Gnomad4 AMR AF: 0.000473

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00167

Gnomad4 FIN AF: 0.0112

Gnomad4 NFE AF: 0.00212

Gnomad4 OTH AF: 0.00

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Oct 11, 2018

- -

Computational scores

Source: dbNSFP v4.3

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: rs750392809; hg19: chr16-31004132;