rs362584

Variant summary

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

The NM_130811.4(SNAP25):​c.-63-1602G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 152,078 control chromosomes in the GnomAD database, including 4,765 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 0.24 ( 4765 hom., cov: 32)

Consequence

SNAP25
NM_130811.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.200
Variant links:
Genes affected
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]
SNAP25-AS1 (HGNC:44312): (SNAP25 antisense RNA 1)

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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=-0.88).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SNAP25NM_130811.4 linkuse as main transcriptc.-63-1602G>A intron_variant ENST00000254976.7 NP_570824.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SNAP25ENST00000254976.7 linkuse as main transcriptc.-63-1602G>A intron_variant 1 NM_130811.4 ENSP00000254976 P5P60880-1
SNAP25-AS1ENST00000421143.6 linkuse as main transcriptn.6-76890C>T intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.243
AC:
36976
AN:
151958
Hom.:
4763
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.166
Gnomad AMI
AF:
0.304
Gnomad AMR
AF:
0.214
Gnomad ASJ
AF:
0.317
Gnomad EAS
AF:
0.185
Gnomad SAS
AF:
0.227
Gnomad FIN
AF:
0.277
Gnomad MID
AF:
0.328
Gnomad NFE
AF:
0.292
Gnomad OTH
AF:
0.249
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.243
AC:
36985
AN:
152078
Hom.:
4765
Cov.:
32
AF XY:
0.243
AC XY:
18031
AN XY:
74326
show subpopulations
Gnomad4 AFR
AF:
0.166
Gnomad4 AMR
AF:
0.214
Gnomad4 ASJ
AF:
0.317
Gnomad4 EAS
AF:
0.185
Gnomad4 SAS
AF:
0.227
Gnomad4 FIN
AF:
0.277
Gnomad4 NFE
AF:
0.292
Gnomad4 OTH
AF:
0.246
Alfa
AF:
0.281
Hom.:
12652
Bravo
AF:
0.234
Asia WGS
AF:
0.187
AC:
650
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
10
DANN
Benign
0.71

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: rs362584; hg19: chr20-10254475; API