16-30992641-C-CGG

Variant summary

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

The NM_052874.5(STX1B):c.*179_*180insCC 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 0.092 (353 hom., cov: 0)
  • Exomes 𝑓: 0.090 (59 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-CGG is Benign according to our data. Variant chr16-30992641-C-CGG is described in ClinVar as [Benign]. Clinvar id is 1240778.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0921 AC: 9078 AN: 98560 Hom.: 353 Cov.: 0

Gnomad AFR AF: 0.0654

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.0696

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.00259

Gnomad SAS AF: 0.0450

Gnomad FIN AF: 0.0959

Gnomad MID AF: 0.119

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.0863

GnomAD4 exome AF: 0.0899 AC: 27034 AN: 300664 Hom.: 59 Cov.: 0 AF XY: 0.0892 AC XY: 13954 AN XY: 156490

Gnomad4 AFR exome AF: 0.0690

Gnomad4 AMR exome AF: 0.0671

Gnomad4 ASJ exome AF: 0.0895

Gnomad4 EAS exome AF: 0.00161

Gnomad4 SAS exome AF: 0.0586

Gnomad4 FIN exome AF: 0.104

Gnomad4 NFE exome AF: 0.106

Gnomad4 OTH exome AF: 0.0925

GnomAD4 genome AF: 0.0920 AC: 9072 AN: 98604 Hom.: 353 Cov.: 0 AF XY: 0.0863 AC XY: 3983 AN XY: 46150

Gnomad4 AFR AF: 0.0652

Gnomad4 AMR AF: 0.0692

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.00260

Gnomad4 SAS AF: 0.0454

Gnomad4 FIN AF: 0.0959

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.0852

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 20, 2019

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Computational scores

Source: dbNSFP v4.3

Splicing

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;