Variant rs362987 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBA1

The NM_130811.4(SNAP25):c.282-121A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 1,463,396 control chromosomes in the GnomAD database, including 172,744 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.51 ( 20130 hom., cov: 33)

Exomes 𝑓: 0.48 ( 152614 hom. )

Consequence

SNAP25
NM_130811.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.65

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 links:

SNAP25-AS1 (HGNC:44312): (SNAP25 antisense RNA 1)

SNAP25-AS1 links:

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=-0.45).

BP6

Variant 20-10296804-A-C is Benign according to our data. Variant chr20-10296804-A-C is described in ClinVar as [Benign]. Clinvar id is 1246499.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNAP25	NM_130811.4 linkuse as main transcript	c.282-121A>C		intron_variant		ENST00000254976.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNAP25	ENST00000254976.7 linkuse as main transcript	c.282-121A>C		intron_variant		1	NM_130811.4	P5	P60880-1
SNAP25-AS1	ENST00000421143.6 linkuse as main transcript	n.5+71911T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.510

AC:

77500

AN:

151956

Hom.:

20090

Cov.:

show subpopulations

Gnomad AFR

AF:

0.569

Gnomad AMI

AF:

0.449

Gnomad AMR

AF:

0.525

Gnomad ASJ

AF:

0.556

Gnomad EAS

AF:

0.295

Gnomad SAS

AF:

0.433

Gnomad FIN

AF:

0.495

Gnomad MID

AF:

0.551

Gnomad NFE

AF:

0.493

Gnomad OTH

AF:

0.515

GnomAD4 exome

AF:

0.480

AC:

629680

AN:

1311322

Hom.:

152614

Cov.:

AF XY:

0.480

AC XY:

312426

AN XY:

651024

show subpopulations

Gnomad4 AFR exome

AF:

0.573

Gnomad4 AMR exome

AF:

0.535

Gnomad4 ASJ exome

AF:

0.551

Gnomad4 EAS exome

AF:

0.363

Gnomad4 SAS exome

AF:

0.459

Gnomad4 FIN exome

AF:

0.494

Gnomad4 NFE exome

AF:

0.479

Gnomad4 OTH exome

AF:

0.480

GnomAD4 genome

AF:

0.510

AC:

77602

AN:

152074

Hom.:

20130

Cov.:

AF XY:

0.509

AC XY:

37820

AN XY:

74328

show subpopulations

Gnomad4 AFR

AF:

0.570

Gnomad4 AMR

AF:

0.525

Gnomad4 ASJ

AF:

0.556

Gnomad4 EAS

AF:

0.297

Gnomad4 SAS

AF:

0.433

Gnomad4 FIN

AF:

0.495

Gnomad4 NFE

AF:

0.493

Gnomad4 OTH

AF:

0.509

Alfa

AF:

0.512

Hom.:

5765

Bravo

AF:

0.517

Asia WGS

AF:

0.380

AC:

1321

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 08, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.45

CADD

Benign

DANN

Benign

0.78

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over