16-30992693-G-GGGGGTGGAGGA

Variant summary

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

The NM_052874.5(STX1B):c.*127_*128insTCCTCCACCCC 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 0.96 (44481 hom., cov: 0)
  • Exomes 𝑓: 0.99 (207195 hom.)
• Consequence: STX1B NM_052874.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.102

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 16-30992693-G-GGGGGTGGAGGA is Benign according to our data. Variant chr16-30992693-G-GGGGGTGGAGGA is described in ClinVar as [Benign]. Clinvar id is 1291868.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STX1B	NM_052874.5	c.*127_*128insTCCTCCACCCC		3_prime_UTR_variant	10/10	ENST00000215095.11
STX1B	XM_017022893.2	c.*127_*128insTCCTCCACCCC		3_prime_UTR_variant	10/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STX1B	ENST00000215095.11	c.*127_*128insTCCTCCACCCC		3_prime_UTR_variant	10/10	1	NM_052874.5	P1

Frequencies

GnomAD3 genomes AF: 0.960 AC: 92507 AN: 96338 Hom.: 44450 Cov.: 0

Gnomad AFR AF: 0.907

Gnomad AMI AF: 0.995

Gnomad AMR AF: 0.973

Gnomad ASJ AF: 0.973

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.977

Gnomad FIN AF: 0.962

Gnomad MID AF: 0.986

Gnomad NFE AF: 0.975

Gnomad OTH AF: 0.969

GnomAD4 exome AF: 0.994 AC: 417026 AN: 419692 Hom.: 207195 Cov.: 6 AF XY: 0.994 AC XY: 218784 AN XY: 220134

Gnomad4 AFR exome AF: 0.940

Gnomad4 AMR exome AF: 0.993

Gnomad4 ASJ exome AF: 0.996

Gnomad4 EAS exome AF: 0.999

Gnomad4 SAS exome AF: 0.992

Gnomad4 FIN exome AF: 0.996

Gnomad4 NFE exome AF: 0.995

Gnomad4 OTH exome AF: 0.992

GnomAD4 genome AF: 0.960 AC: 92578 AN: 96418 Hom.: 44481 Cov.: 0 AF XY: 0.962 AC XY: 43134 AN XY: 44848

Gnomad4 AFR AF: 0.907

Gnomad4 AMR AF: 0.973

Gnomad4 ASJ AF: 0.973

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.977

Gnomad4 FIN AF: 0.962

Gnomad4 NFE AF: 0.975

Gnomad4 OTH AF: 0.970

Alfa AF: 0.608 Hom.: 2185

Asia WGS AF: 0.975 AC: 3303 AN: 3386

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

Jul 09, 2018

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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: rs11269803; hg19: chr16-31004014;