chr6-32193653-C-A

Variant names:

• chr6-32193653-C-A
• rs204990
• ENST00000375043.3:c.-101-529G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_022107.3(GPSM3):​c.-101-529G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 151,872 control chromosomes in the GnomAD database, including 3,600 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 0.21 (3600 hom., cov: 32)
• Consequence: GPSM3 NM_022107.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0930
• Publications: 42 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022107.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPSM3	NM_022107.3		c.-101-529G>T		intron	N/A	NP_071390.1	Q9Y4H4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPSM3	ENST00000375043.3	TSL:1	c.-101-529G>T		intron	N/A	ENSP00000364183.3	Q9Y4H4

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31873 AN: 151754 Hom.: 3606 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.190

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.210 AC: 31884 AN: 151872 Hom.: 3600 Cov.: 32 AF XY: 0.205 AC XY: 15236 AN XY: 74214

African (AFR) AF: 0.272 AC: 11241 AN: 41360

American (AMR) AF: 0.156 AC: 2383 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 561 AN: 3470

East Asian (EAS) AF: 0.301 AC: 1557 AN: 5170

South Asian (SAS) AF: 0.194 AC: 939 AN: 4832

European-Finnish (FIN) AF: 0.146 AC: 1536 AN: 10496

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13111 AN: 67968

Other (OTH) AF: 0.190 AC: 401 AN: 2106

Alfa AF: 0.201 Hom.: 10338

Bravo AF: 0.214

Asia WGS AF: 0.221 AC: 769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.27
PhyloP100		-0.093
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs204990; hg19: chr6-32161430;