rs11787792

chr9-136357696-G-Achr9-136357696-G-Cchr9-136357696-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001145638.3(GPSM1):c.1822-318G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.695 in 152,192 control chromosomes in the GnomAD database, including 37,230 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 0.70 (37230 hom., cov: 35)
• Consequence: GPSM1 NM_001145638.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.603

Genes affected

GPSM1 (HGNC:17858): (G protein signaling modulator 1) G-protein signaling modulators (GPSMs) play diverse functional roles through their interaction with G-protein subunits. This gene encodes a receptor-independent activator of G protein signaling, which is one of several factors that influence the basal activity of G-protein signaling systems. The protein contains seven tetratricopeptide repeats in its N-terminal half and four G-protein regulatory (GPR) motifs in its C-terminal half. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.918 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPSM1	NM_001145638.3	c.1822-318G>A		intron_variant		ENST00000440944.6
GPSM1	NM_001145639.2	c.295-318G>A		intron_variant
GPSM1	NM_001200003.2	c.295-318G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPSM1	ENST00000440944.6	c.1822-318G>A		intron_variant		5	NM_001145638.3	P1

Frequencies

GnomAD3 genomes AF: 0.695 AC: 105733 AN: 152074 Hom.: 37199 Cov.: 35

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.940

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.693

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

GnomAD4 genome AF: 0.695 AC: 105812 AN: 152192 Hom.: 37230 Cov.: 35 AF XY: 0.695 AC XY: 51743 AN XY: 74402

Gnomad4 AFR AF: 0.767

Gnomad4 AMR AF: 0.594

Gnomad4 ASJ AF: 0.661

Gnomad4 EAS AF: 0.940

Gnomad4 SAS AF: 0.759

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.664

Gnomad4 OTH AF: 0.693

Alfa AF: 0.543 Hom.: 1421

Bravo AF: 0.698

Asia WGS AF: 0.815 AC: 2835 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.54
Dann	Benign	0.51

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

Other links and lift over

dbSNP: rs11787792; hg19: chr9-139252148;