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rs1569061

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004603.4(STX1A):​c.*256G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0795 in 563,168 control chromosomes in the GnomAD database, including 2,230 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 0.099 ( 941 hom., cov: 32)
Exomes 𝑓: 0.072 ( 1289 hom. )

Consequence

STX1A
NM_004603.4 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0740
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
STX1ANM_004603.4 linkuse as main transcriptc.*256G>A 3_prime_UTR_variant 10/10 ENST00000222812.8
STX1ANM_001165903.2 linkuse as main transcriptc.*321G>A 3_prime_UTR_variant 10/10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
STX1AENST00000222812.8 linkuse as main transcriptc.*256G>A 3_prime_UTR_variant 10/101 NM_004603.4 P1Q16623-1
STX1AENST00000395156.7 linkuse as main transcriptc.*321G>A 3_prime_UTR_variant 10/101 Q16623-3
STX1AENST00000484736.5 linkuse as main transcriptn.536G>A non_coding_transcript_exon_variant 2/22

Frequencies

GnomAD3 genomes
AF:
0.0986
AC:
14993
AN:
152072
Hom.:
934
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.160
Gnomad AMI
AF:
0.123
Gnomad AMR
AF:
0.121
Gnomad ASJ
AF:
0.0865
Gnomad EAS
AF:
0.0259
Gnomad SAS
AF:
0.0744
Gnomad FIN
AF:
0.0457
Gnomad MID
AF:
0.114
Gnomad NFE
AF:
0.0716
Gnomad OTH
AF:
0.100
GnomAD4 exome
AF:
0.0724
AC:
29775
AN:
410978
Hom.:
1289
Cov.:
3
AF XY:
0.0729
AC XY:
15779
AN XY:
216400
show subpopulations
Gnomad4 AFR exome
AF:
0.161
Gnomad4 AMR exome
AF:
0.126
Gnomad4 ASJ exome
AF:
0.0776
Gnomad4 EAS exome
AF:
0.0212
Gnomad4 SAS exome
AF:
0.0763
Gnomad4 FIN exome
AF:
0.0447
Gnomad4 NFE exome
AF:
0.0709
Gnomad4 OTH exome
AF:
0.0860
GnomAD4 genome
AF:
0.0987
AC:
15016
AN:
152190
Hom.:
941
Cov.:
32
AF XY:
0.0976
AC XY:
7265
AN XY:
74412
show subpopulations
Gnomad4 AFR
AF:
0.160
Gnomad4 AMR
AF:
0.122
Gnomad4 ASJ
AF:
0.0865
Gnomad4 EAS
AF:
0.0260
Gnomad4 SAS
AF:
0.0747
Gnomad4 FIN
AF:
0.0457
Gnomad4 NFE
AF:
0.0716
Gnomad4 OTH
AF:
0.0994
Alfa
AF:
0.0874
Hom.:
464
Bravo
AF:
0.109
Asia WGS
AF:
0.0640
AC:
224
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
6.4
DANN
Benign
0.65

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

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

Other links and lift over

dbSNP: rs1569061; hg19: chr7-73114481; API