6-32190542-A-G

Variant names:

• chr6-32190542-A-G
• rs176095
• ENST00000809038.1:n.293A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000809038.1(ENSG00000305139):​n.293A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 151,544 control chromosomes in the GnomAD database, including 3,939 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 0.22 (3939 hom., cov: 30)
• Consequence: ENSG00000305139 ENST00000809038.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.39
• Publications: 65 publications found

Genes affected

ENSG00000305139 (HGNC:):

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000809038.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPSM3	NM_001276501.2	MANE Select	c.*824T>C		downstream_gene	N/A	NP_001263430.1
	GPSM3	NM_022107.3		c.*824T>C		downstream_gene	N/A	NP_071390.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305139	ENST00000809038.1		n.293A>G		non_coding_transcript_exon	Exon 1 of 1
	GPSM3	ENST00000375040.8	TSL:1 MANE Select	c.*824T>C		downstream_gene	N/A	ENSP00000364180.3
	GPSM3	ENST00000375043.3	TSL:1	c.*824T>C		downstream_gene	N/A	ENSP00000364183.3

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33540 AN: 151422 Hom.: 3946 Cov.: 30

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.221 AC: 33547 AN: 151544 Hom.: 3939 Cov.: 30 AF XY: 0.214 AC XY: 15804 AN XY: 74018

African (AFR) AF: 0.280 AC: 11560 AN: 41260

American (AMR) AF: 0.150 AC: 2281 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 399 AN: 3468

East Asian (EAS) AF: 0.208 AC: 1057 AN: 5078

South Asian (SAS) AF: 0.194 AC: 933 AN: 4798

European-Finnish (FIN) AF: 0.137 AC: 1446 AN: 10524

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15161 AN: 67864

Other (OTH) AF: 0.203 AC: 427 AN: 2104

Alfa AF: 0.224 Hom.: 14504

Bravo AF: 0.228

Asia WGS AF: 0.209 AC: 725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	17
DANN	Benign	0.89
PhyloP100		2.4
PromoterAI		0.099	Neutral

Splicing

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

Other links and lift over

dbSNP: rs176095; hg19: chr6-32158319;