Variant 6-32192154-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001276501.2(GPSM3):c.139C>G(p.His47Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00672 in 1,509,708 control chromosomes in the GnomAD database, including 97 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0070 ( 6 hom., cov: 31)

Exomes 𝑓: 0.0067 ( 91 hom. )

Consequence

GPSM3
NM_001276501.2 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.980

Variant links:

Genes affected

GPSM3 (HGNC:13945): (G protein signaling modulator 3) Predicted to enable GTPase regulator activity. Predicted to be involved in positive regulation of inflammatory response. Predicted to act upstream of or within positive regulation of cytokine production involved in inflammatory response and positive regulation of leukocyte chemotaxis. Predicted to be located in cytoplasm and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

GPSM3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.004505217).

BP6

Variant 6-32192154-G-C is Benign according to our data. Variant chr6-32192154-G-C is described in ClinVar as [Benign]. Clinvar id is 772877.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.0744 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPSM3	NM_001276501.2 linkuse as main transcript	c.139C>G	p.His47Asp	missense_variant	2/4	ENST00000375040.8	NP_001263430.1
GPSM3	NM_022107.3 linkuse as main transcript	c.139C>G	p.His47Asp	missense_variant	6/8		NP_071390.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPSM3	ENST00000375040.8 linkuse as main transcript	c.139C>G	p.His47Asp	missense_variant	2/4	1	NM_001276501.2	ENSP00000364180	P1

Frequencies

GnomAD3 genomes

AF:

0.00706

AC:

1072

AN:

151938

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00878

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00759

Gnomad ASJ

AF:

0.0179

Gnomad EAS

AF:

0.00174

Gnomad SAS

AF:

0.00912

Gnomad FIN

AF:

0.00113

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.00590

Gnomad OTH

AF:

0.0187

GnomAD3 exomes

AF:

0.00655

AC:

1139

AN:

173834

Hom.:

AF XY:

0.00687

AC XY:

629

AN XY:

91508

show subpopulations

Gnomad AFR exome

AF:

0.0101

Gnomad AMR exome

AF:

0.00571

Gnomad ASJ exome

AF:

0.0220

Gnomad EAS exome

AF:

0.00111

Gnomad SAS exome

AF:

0.0121

Gnomad FIN exome

AF:

0.00120

Gnomad NFE exome

AF:

0.00657

Gnomad OTH exome

AF:

0.00796

GnomAD4 exome

AF:

0.00669

AC:

9083

AN:

1357652

Hom.:

Cov.:

AF XY:

0.00695

AC XY:

4613

AN XY:

664208

show subpopulations

Gnomad4 AFR exome

AF:

0.00865

Gnomad4 AMR exome

AF:

0.00665

Gnomad4 ASJ exome

AF:

0.0203

Gnomad4 EAS exome

AF:

0.000756

Gnomad4 SAS exome

AF:

0.0117

Gnomad4 FIN exome

AF:

0.00149

Gnomad4 NFE exome

AF:

0.00604

Gnomad4 OTH exome

AF:

0.00891

GnomAD4 genome

AF:

0.00701

AC:

1066

AN:

152056

Hom.:

Cov.:

AF XY:

0.00721

AC XY:

536

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.00878

Gnomad4 AMR

AF:

0.00758

Gnomad4 ASJ

AF:

0.0179

Gnomad4 EAS

AF:

0.00175

Gnomad4 SAS

AF:

0.00912

Gnomad4 FIN

AF:

0.00113

Gnomad4 NFE

AF:

0.00590

Gnomad4 OTH

AF:

0.0180

Alfa

AF:

0.00619

Hom.:

Bravo

AF:

0.00725

ESP6500AA

AF:

0.00817

AC:

ESP6500EA

AF:

0.00686

AC:

ExAC

AF:

0.00651

AC:

748

Asia WGS

AF:

0.00751

AC:

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

Labcorp Genetics (formerly Invitae), Labcorp

May 25, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.089

BayesDel_addAF

Benign

-0.49

BayesDel_noAF

Benign

-0.46

CADD

Benign

DANN

Benign

0.55

DEOGEN2

Benign

0.014

T;T;T

Eigen

Benign

-0.98

Eigen_PC

Benign

-0.95

FATHMM_MKL

Benign

0.29

LIST_S2

Benign

0.60

T;.;.

MetaRNN

Benign

0.0045

T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.81

.;L;L

MutationTaster

Benign

0.79

N;N;N

PrimateAI

Uncertain

0.69

PROVEAN

Benign

0.090

N;N;N

REVEL

Benign

0.023

Sift

Benign

0.084

T;T;T

Sift4G

Benign

0.83

T;T;T

Polyphen

0.0010

.;B;B

Vest4

0.30

MVP

0.043

MPC

0.62

ClinPred

0.0016

GERP RS

1.8

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Varity_R

0.072

gMVP

0.20

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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