rs11787792

Variant names:

• chr9-136357696-G-A
• rs11787792
• NM_001145638.3:c.1822-318G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-136357696-G-A
• chr9-136357696-G-C
• chr9-136357696-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 50 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
GPSM1	NM_001145638.3	c.1822-318G>A		intron_variant	Intron 13 of 13	ENST00000440944.6	NP_001139110.2
GPSM1	NM_001145639.2	c.295-318G>A		intron_variant	Intron 3 of 3		NP_001139111.1
GPSM1	NM_001200003.2	c.295-318G>A		intron_variant	Intron 3 of 3		NP_001186932.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPSM1	ENST00000440944.6	c.1822-318G>A		intron_variant	Intron 13 of 13	5	NM_001145638.3	ENSP00000392828.1

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

African (AFR) AF: 0.767 AC: 31849 AN: 41536

American (AMR) AF: 0.594 AC: 9082 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.661 AC: 2295 AN: 3470

East Asian (EAS) AF: 0.940 AC: 4860 AN: 5172

South Asian (SAS) AF: 0.759 AC: 3669 AN: 4832

European-Finnish (FIN) AF: 0.633 AC: 6721 AN: 10616

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.664 AC: 45130 AN: 67954

Other (OTH) AF: 0.693 AC: 1463 AN: 2112

Alfa AF: 0.665 Hom.: 7917

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
PhyloP100		-0.60
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11787792; hg19: chr9-139252148;