7-73708626-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_004603.4(STX1A):c.171G>A(p.Lys57Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000291 in 1,614,188 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00022 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00030 ( 1 hom. )
Consequence
STX1A
NM_004603.4 synonymous
NM_004603.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.575
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.43).
BP6
Variant 7-73708626-C-T is Benign according to our data. Variant chr7-73708626-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3771342.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.575 with no splicing effect.
BS2
High AC in GnomAd4 at 33 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
STX1A | NM_004603.4 | c.171G>A | p.Lys57Lys | synonymous_variant | Exon 3 of 10 | ENST00000222812.8 | NP_004594.1 | |
STX1A | NM_001165903.2 | c.171G>A | p.Lys57Lys | synonymous_variant | Exon 3 of 10 | NP_001159375.1 | ||
STX1A | XM_047420777.1 | c.171G>A | p.Lys57Lys | synonymous_variant | Exon 3 of 9 | XP_047276733.1 | ||
STX1A | XM_047420778.1 | c.171G>A | p.Lys57Lys | synonymous_variant | Exon 3 of 9 | XP_047276734.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000223 AC: 34AN: 152252Hom.: 0 Cov.: 32
GnomAD3 genomes
AF:
AC:
34
AN:
152252
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.000307 AC: 77AN: 251078Hom.: 0 AF XY: 0.000295 AC XY: 40AN XY: 135756
GnomAD3 exomes
AF:
AC:
77
AN:
251078
Hom.:
AF XY:
AC XY:
40
AN XY:
135756
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000298 AC: 436AN: 1461818Hom.: 1 Cov.: 35 AF XY: 0.000287 AC XY: 209AN XY: 727202
GnomAD4 exome
AF:
AC:
436
AN:
1461818
Hom.:
Cov.:
35
AF XY:
AC XY:
209
AN XY:
727202
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.000217 AC: 33AN: 152370Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74508
GnomAD4 genome
AF:
AC:
33
AN:
152370
Hom.:
Cov.:
32
AF XY:
AC XY:
16
AN XY:
74508
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Feb 01, 2025
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
STX1A: BP4, BP7 -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at