rs6104567

Variant summary

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

The NR_040710.1(SNAP25-AS1):​n.270+4452A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 152,122 control chromosomes in the GnomAD database, including 6,211 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 0.27 ( 6211 hom., cov: 33)

Consequence

SNAP25-AS1
NR_040710.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.69
Variant links:
Genes affected
SNAP25-AS1 (HGNC:44312): (SNAP25 antisense RNA 1)
SNAP25 (HGNC:11132): (synaptosome associated protein 25) Synaptic vesicle membrane docking and fusion is mediated by SNAREs (soluble N-ethylmaleimide-sensitive factor attachment protein receptors) located on the vesicle membrane (v-SNAREs) and the target membrane (t-SNAREs). The assembled v-SNARE/t-SNARE complex consists of a bundle of four helices, one of which is supplied by v-SNARE and the other three by t-SNARE. For t-SNAREs on the plasma membrane, the protein syntaxin supplies one helix and the protein encoded by this gene contributes the other two. Therefore, this gene product is a presynaptic plasma membrane protein involved in the regulation of neurotransmitter release. Two alternative transcript variants encoding different protein isoforms have been described for this gene. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SNAP25-AS1NR_040710.1 linkuse as main transcriptn.270+4452A>C intron_variant, non_coding_transcript_variant
LOC124904959XR_007067723.1 linkuse as main transcriptn.377-341T>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SNAP25-AS1ENST00000421143.6 linkuse as main transcriptn.6-17848A>C intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.266
AC:
40431
AN:
152002
Hom.:
6194
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.151
Gnomad AMI
AF:
0.196
Gnomad AMR
AF:
0.402
Gnomad ASJ
AF:
0.206
Gnomad EAS
AF:
0.546
Gnomad SAS
AF:
0.380
Gnomad FIN
AF:
0.387
Gnomad MID
AF:
0.225
Gnomad NFE
AF:
0.261
Gnomad OTH
AF:
0.269
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.266
AC:
40466
AN:
152122
Hom.:
6211
Cov.:
33
AF XY:
0.279
AC XY:
20715
AN XY:
74364
show subpopulations
Gnomad4 AFR
AF:
0.151
Gnomad4 AMR
AF:
0.403
Gnomad4 ASJ
AF:
0.206
Gnomad4 EAS
AF:
0.547
Gnomad4 SAS
AF:
0.378
Gnomad4 FIN
AF:
0.387
Gnomad4 NFE
AF:
0.261
Gnomad4 OTH
AF:
0.271
Alfa
AF:
0.264
Hom.:
8162
Bravo
AF:
0.266

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.14
DANN
Benign
0.65

Splicing

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: rs6104567; hg19: chr20-10195433; API