Variant 6-32191414-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_001276501.2(GPSM3):c.435G>A(p.Gly145=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00481 in 1,593,600 control chromosomes in the GnomAD database, including 82 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0047 ( 10 hom., cov: 31)

Exomes 𝑓: 0.0048 ( 72 hom. )

Consequence

GPSM3
NM_001276501.2 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.889

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 -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BP6

Variant 6-32191414-C-T is Benign according to our data. Variant chr6-32191414-C-T is described in ClinVar as [Benign]. Clinvar id is 770360.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.889 with no splicing effect.

BS1

Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00481 (6938/1441414) while in subpopulation MID AF= 0.0165 (94/5698). AF 95% confidence interval is 0.0151. There are 72 homozygotes in gnomad4_exome. There are 3784 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 10 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPSM3	NM_001276501.2 linkuse as main transcript	c.435G>A	p.Gly145=	synonymous_variant	4/4	ENST00000375040.8
GPSM3	NM_022107.3 linkuse as main transcript	c.435G>A	p.Gly145=	synonymous_variant	8/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPSM3	ENST00000375040.8 linkuse as main transcript	c.435G>A	p.Gly145=	synonymous_variant	4/4	1	NM_001276501.2	P1

Frequencies

GnomAD3 genomes

AF:

0.00472

AC:

718

AN:

152068

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00135

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00812

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00987

Gnomad SAS

AF:

0.0158

Gnomad FIN

AF:

0.00424

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.00500

Gnomad OTH

AF:

0.0101

GnomAD3 exomes

AF:

0.00657

AC:

1543

AN:

234894

Hom.:

AF XY:

0.00707

AC XY:

905

AN XY:

127938

show subpopulations

Gnomad AFR exome

AF:

0.00116

Gnomad AMR exome

AF:

0.00744

Gnomad ASJ exome

AF:

0.000324

Gnomad EAS exome

AF:

0.00743

Gnomad SAS exome

AF:

0.0155

Gnomad FIN exome

AF:

0.00380

Gnomad NFE exome

AF:

0.00569

Gnomad OTH exome

AF:

0.00689

GnomAD4 exome

AF:

0.00481

AC:

6938

AN:

1441414

Hom.:

Cov.:

AF XY:

0.00528

AC XY:

3784

AN XY:

716870

show subpopulations

Gnomad4 AFR exome

AF:

0.00119

Gnomad4 AMR exome

AF:

0.00988

Gnomad4 ASJ exome

AF:

0.000197

Gnomad4 EAS exome

AF:

0.00432

Gnomad4 SAS exome

AF:

0.0158

Gnomad4 FIN exome

AF:

0.00361

Gnomad4 NFE exome

AF:

0.00378

Gnomad4 OTH exome

AF:

0.00944

GnomAD4 genome

AF:

0.00474

AC:

722

AN:

152186

Hom.:

Cov.:

AF XY:

0.00464

AC XY:

345

AN XY:

74406

show subpopulations

Gnomad4 AFR

AF:

0.00135

Gnomad4 AMR

AF:

0.00824

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00989

Gnomad4 SAS

AF:

0.0158

Gnomad4 FIN

AF:

0.00424

Gnomad4 NFE

AF:

0.00500

Gnomad4 OTH

AF:

0.0118

Alfa

AF:

0.00396

Hom.:

Bravo

AF:

0.00426

Asia WGS

AF:

0.0400

AC:

137

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

Invitae

May 25, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

6.3

DANN

Benign

0.83

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