Variant rs2241621 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001394390.1(STON2):c.2722T>G(p.Ser908Ala) variant causes a missense change. The variant allele was found at a frequency of 0.558 in 1,613,772 control chromosomes in the GnomAD database, including 256,448 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 0.48 ( 18662 hom., cov: 32)

Exomes 𝑓: 0.57 ( 237786 hom. )

Consequence

STON2
NM_001394390.1 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.34

Variant links:

Genes affected

STON2 (HGNC:30652): (stonin 2) This gene encodes a protein which is a membrane protein involved in regulating endocytotic complexes. The protein product is described as one of the clathrin-associated sorting proteins, adaptor molecules which ensure specific proteins are internalized. The encoded protein has also been shown to participate in synaptic vesicle recycling through interaction with synaptotagmin 1 required for neurotransmission. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]

STON2 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 (MetaRNN=0.0016493797).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STON2	NM_001394390.1 linkuse as main transcript	c.2722T>G	p.Ser908Ala	missense_variant	7/8	ENST00000614646.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STON2	ENST00000614646.5 linkuse as main transcript	c.2722T>G	p.Ser908Ala	missense_variant	7/8	5	NM_001394390.1	P1

Frequencies

GnomAD3 genomes

AF:

0.477

AC:

72509

AN:

151854

Hom.:

18663

Cov.:

show subpopulations

Gnomad AFR

AF:

0.283

Gnomad AMI

AF:

0.531

Gnomad AMR

AF:

0.500

Gnomad ASJ

AF:

0.578

Gnomad EAS

AF:

0.389

Gnomad SAS

AF:

0.550

Gnomad FIN

AF:

0.499

Gnomad MID

AF:

0.627

Gnomad NFE

AF:

0.581

Gnomad OTH

AF:

0.520

GnomAD3 exomes

AF:

0.524

AC:

131729

AN:

251472

Hom.:

35640

AF XY:

0.535

AC XY:

72759

AN XY:

135912

show subpopulations

Gnomad AFR exome

AF:

0.275

Gnomad AMR exome

AF:

0.470

Gnomad ASJ exome

AF:

0.582

Gnomad EAS exome

AF:

0.384

Gnomad SAS exome

AF:

0.568

Gnomad FIN exome

AF:

0.505

Gnomad NFE exome

AF:

0.583

Gnomad OTH exome

AF:

0.560

GnomAD4 exome

AF:

0.566

AC:

828108

AN:

1461800

Hom.:

237786

Cov.:

AF XY:

0.568

AC XY:

412989

AN XY:

727204

show subpopulations

Gnomad4 AFR exome

AF:

0.269

Gnomad4 AMR exome

AF:

0.475

Gnomad4 ASJ exome

AF:

0.582

Gnomad4 EAS exome

AF:

0.433

Gnomad4 SAS exome

AF:

0.569

Gnomad4 FIN exome

AF:

0.501

Gnomad4 NFE exome

AF:

0.588

Gnomad4 OTH exome

AF:

0.541

GnomAD4 genome

AF:

0.477

AC:

72517

AN:

151972

Hom.:

18662

Cov.:

AF XY:

0.477

AC XY:

35392

AN XY:

74274

show subpopulations

Gnomad4 AFR

AF:

0.283

Gnomad4 AMR

AF:

0.499

Gnomad4 ASJ

AF:

0.578

Gnomad4 EAS

AF:

0.389

Gnomad4 SAS

AF:

0.550

Gnomad4 FIN

AF:

0.499

Gnomad4 NFE

AF:

0.581

Gnomad4 OTH

AF:

0.515

Alfa

AF:

0.561

Hom.:

59874

Bravo

AF:

0.467

TwinsUK

AF:

0.596

AC:

2209

ALSPAC

AF:

0.580

AC:

2236

ESP6500AA

AF:

0.292

AC:

1287

ESP6500EA

AF:

0.590

AC:

5070

ExAC

AF:

0.522

AC:

63406

Asia WGS

AF:

0.424

AC:

1475

AN:

3478

EpiCase

AF:

0.597

EpiControl

AF:

0.591

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.52

BayesDel_noAF

Benign

-0.38

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.030

.;.;.;T

Eigen

Uncertain

0.37

Eigen_PC

Uncertain

0.32

FATHMM_MKL

Uncertain

0.88

LIST_S2

Benign

0.44

.;T;T;T

MetaRNN

Benign

0.0016

T;T;T;T

MetaSVM

Benign

-0.94

MutationAssessor

Benign

1.6

L;.;L;L

MutationTaster

Benign

0.0011

P;P

PrimateAI

Uncertain

0.56

PROVEAN

Benign

-1.2

N;.;.;N

REVEL

Benign

0.13

Sift

Benign

0.044

D;.;.;D

Sift4G

Benign

0.37

T;.;T;T

Polyphen

1.0

.;.;.;D

Vest4

0.28

MPC

0.46

ClinPred

0.033

GERP RS

4.4

Varity_R

0.11

gMVP

0.19

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