Variant 1-227748061-G-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_053052.4(SNAP47):c.325G>A(p.Val109Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0665 in 1,614,044 control chromosomes in the GnomAD database, including 6,454 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.082 ( 805 hom., cov: 33)

Exomes 𝑓: 0.065 ( 5649 hom. )

Consequence

SNAP47
NM_053052.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.68

Variant links:

Genes affected

SNAP47 (HGNC:30669): (synaptosome associated protein 47) Predicted to enable SNAP receptor activity and syntaxin binding activity. Predicted to be involved in synaptic vesicle fusion to presynaptic active zone membrane and synaptic vesicle priming. Predicted to act upstream of or within long-term synaptic potentiation. Colocalizes with BLOC-1 complex. [provided by Alliance of Genome Resources, Apr 2022]

SNAP47 links:

SNAP47 (HGNC:):

SNAP47 links:

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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 (MetaRNN=0.0048897266).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNAP47	NM_053052.4 linkuse as main transcript	c.325G>A	p.Val109Met	missense_variant	2/5	ENST00000617596.5	NP_444280.3	Q5SQN1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNAP47	ENST00000617596.5 linkuse as main transcript	c.325G>A	p.Val109Met	missense_variant	2/5	1	NM_053052.4	ENSP00000483253.1		A0A087X0B7

Frequencies

GnomAD3 genomes

AF:

0.0821

AC:

12484

AN:

152112

Hom.:

803

Cov.:

show subpopulations

Gnomad AFR

AF:

0.103

Gnomad AMI

AF:

0.0439

Gnomad AMR

AF:

0.123

Gnomad ASJ

AF:

0.0389

Gnomad EAS

AF:

0.330

Gnomad SAS

AF:

0.118

Gnomad FIN

AF:

0.0586

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.0451

Gnomad OTH

AF:

0.0761

GnomAD3 exomes

AF:

0.106

AC:

26499

AN:

251110

Hom.:

2494

AF XY:

0.0987

AC XY:

13403

AN XY:

135764

show subpopulations

Gnomad AFR exome

AF:

0.111

Gnomad AMR exome

AF:

0.230

Gnomad ASJ exome

AF:

0.0515

Gnomad EAS exome

AF:

0.326

Gnomad SAS exome

AF:

0.111

Gnomad FIN exome

AF:

0.0560

Gnomad NFE exome

AF:

0.0459

Gnomad OTH exome

AF:

0.0680

GnomAD4 exome

AF:

0.0649

AC:

94812

AN:

1461814

Hom.:

5649

Cov.:

AF XY:

0.0652

AC XY:

47414

AN XY:

727202

show subpopulations

Gnomad4 AFR exome

AF:

0.109

Gnomad4 AMR exome

AF:

0.214

Gnomad4 ASJ exome

AF:

0.0487

Gnomad4 EAS exome

AF:

0.323

Gnomad4 SAS exome

AF:

0.111

Gnomad4 FIN exome

AF:

0.0577

Gnomad4 NFE exome

AF:

0.0450

Gnomad4 OTH exome

AF:

0.0718

GnomAD4 genome

AF:

0.0822

AC:

12510

AN:

152230

Hom.:

805

Cov.:

AF XY:

0.0842

AC XY:

6267

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.103

Gnomad4 AMR

AF:

0.124

Gnomad4 ASJ

AF:

0.0389

Gnomad4 EAS

AF:

0.331

Gnomad4 SAS

AF:

0.118

Gnomad4 FIN

AF:

0.0586

Gnomad4 NFE

AF:

0.0452

Gnomad4 OTH

AF:

0.0754

Alfa

AF:

0.0594

Hom.:

1070

Bravo

AF:

0.0929

TwinsUK

AF:

0.0413

AC:

153

ALSPAC

AF:

0.0493

AC:

190

ESP6500AA

AF:

0.109

AC:

479

ESP6500EA

AF:

0.0453

AC:

390

ExAC

AF:

0.100

AC:

12147

Asia WGS

AF:

0.203

AC:

709

AN:

3478

EpiCase

AF:

0.0469

EpiControl

AF:

0.0483

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.079

BayesDel_addAF

Benign

-0.66

BayesDel_noAF

Benign

-0.57

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.0012

T;T;T

Eigen

Benign

-0.68

Eigen_PC

Benign

-0.83

FATHMM_MKL

Benign

0.16

LIST_S2

Benign

0.32

.;T;T

MetaRNN

Benign

0.0049

T;T;T

MetaSVM

Benign

-0.97

MutationAssessor

Benign

1.0

L;L;.

PrimateAI

Uncertain

0.57

PROVEAN

Benign

-0.51

N;N;.

REVEL

Benign

0.18

Sift

Benign

0.22

T;T;.

Sift4G

Benign

0.13

T;T;T

Polyphen

0.98

D;D;.

Vest4

0.024

MPC

0.14

ClinPred

0.0050

GERP RS

1.0

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.020

gMVP

0.30

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over