Variant rs2228607 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The ENST00000222812.8(STX1A):c.204T>C(p.Asp68=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 1,612,352 control chromosomes in the GnomAD database, including 239,418 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.53 ( 21310 hom., cov: 33)

Exomes 𝑓: 0.54 ( 218108 hom. )

Consequence

STX1A
ENST00000222812.8 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.16

Variant links:

Genes affected

STX1A (HGNC:11433): (syntaxin 1A) This gene encodes a member of the syntaxin superfamily. Syntaxins are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane. Syntaxins possess a single C-terminal transmembrane domain, a SNARE [Soluble NSF (N-ethylmaleimide-sensitive fusion protein)-Attachment protein REceptor] domain (known as H3), and an N-terminal regulatory domain (Habc). Syntaxins bind synaptotagmin in a calcium-dependent fashion and interact with voltage dependent calcium and potassium channels via the C-terminal H3 domain. This gene product is a key molecule in ion channel regulation and synaptic exocytosis. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Sep 2009]

STX1A links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.7).

BP7

Synonymous conserved (PhyloP=-3.16 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
STX1A	NM_004603.4 linkuse as main transcript	c.204T>C	p.Asp68=	synonymous_variant	3/10	ENST00000222812.8	NP_004594.1
STX1A	NM_001165903.2 linkuse as main transcript	c.204T>C	p.Asp68=	synonymous_variant	3/10		NP_001159375.1
STX1A	XM_047420777.1 linkuse as main transcript	c.204T>C	p.Asp68=	synonymous_variant	3/9		XP_047276733.1
STX1A	XM_047420778.1 linkuse as main transcript	c.204T>C	p.Asp68=	synonymous_variant	3/9		XP_047276734.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STX1A	ENST00000222812.8 linkuse as main transcript	c.204T>C	p.Asp68=	synonymous_variant	3/10	1	NM_004603.4	ENSP00000222812	P1	Q16623-1

Frequencies

GnomAD3 genomes

AF:

0.527

AC:

80031

AN:

152004

Hom.:

21294

Cov.:

show subpopulations

Gnomad AFR

AF:

0.501

Gnomad AMI

AF:

0.571

Gnomad AMR

AF:

0.476

Gnomad ASJ

AF:

0.634

Gnomad EAS

AF:

0.431

Gnomad SAS

AF:

0.421

Gnomad FIN

AF:

0.520

Gnomad MID

AF:

0.677

Gnomad NFE

AF:

0.562

Gnomad OTH

AF:

0.543

GnomAD3 exomes

AF:

0.515

AC:

127851

AN:

248296

Hom.:

33476

AF XY:

0.517

AC XY:

69448

AN XY:

134338

show subpopulations

Gnomad AFR exome

AF:

0.502

Gnomad AMR exome

AF:

0.425

Gnomad ASJ exome

AF:

0.631

Gnomad EAS exome

AF:

0.429

Gnomad SAS exome

AF:

0.439

Gnomad FIN exome

AF:

0.523

Gnomad NFE exome

AF:

0.565

Gnomad OTH exome

AF:

0.550

GnomAD4 exome

AF:

0.544

AC:

794674

AN:

1460230

Hom.:

218108

Cov.:

AF XY:

0.542

AC XY:

393799

AN XY:

726334

show subpopulations

Gnomad4 AFR exome

AF:

0.507

Gnomad4 AMR exome

AF:

0.437

Gnomad4 ASJ exome

AF:

0.627

Gnomad4 EAS exome

AF:

0.410

Gnomad4 SAS exome

AF:

0.442

Gnomad4 FIN exome

AF:

0.524

Gnomad4 NFE exome

AF:

0.560

Gnomad4 OTH exome

AF:

0.551

GnomAD4 genome

AF:

0.526

AC:

80089

AN:

152122

Hom.:

21310

Cov.:

AF XY:

0.523

AC XY:

38864

AN XY:

74354

show subpopulations

Gnomad4 AFR

AF:

0.501

Gnomad4 AMR

AF:

0.476

Gnomad4 ASJ

AF:

0.634

Gnomad4 EAS

AF:

0.431

Gnomad4 SAS

AF:

0.423

Gnomad4 FIN

AF:

0.520

Gnomad4 NFE

AF:

0.562

Gnomad4 OTH

AF:

0.544

Alfa

AF:

0.556

Hom.:

12005

Bravo

AF:

0.525

Asia WGS

AF:

0.411

AC:

1431

AN:

3478

EpiCase

AF:

0.575

EpiControl

AF:

0.567

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

0.37

DANN

Benign

0.61

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over