rs3812550

Variant names:

• chr9-136358427-A-G
• rs3812550
• NM_001145638.3:c.*207A>G

Variant summary

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

The NM_001145638.3(GPSM1):​c.*207A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 577,946 control chromosomes in the GnomAD database, including 59,488 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 0.43 (14246 hom., cov: 35)
  • Exomes 𝑓: 0.45 (45242 hom.)
• Consequence: GPSM1 NM_001145638.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.49
• Publications: 23 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.492 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPSM1	NM_001145638.3	c.*207A>G		3_prime_UTR_variant	Exon 14 of 14	ENST00000440944.6	NP_001139110.2
GPSM1	NM_001145639.2	c.*207A>G		3_prime_UTR_variant	Exon 4 of 4		NP_001139111.1
GPSM1	NM_001200003.2	c.*207A>G		3_prime_UTR_variant	Exon 4 of 4		NP_001186932.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPSM1	ENST00000440944.6	c.*207A>G		3_prime_UTR_variant	Exon 14 of 14	5	NM_001145638.3	ENSP00000392828.1

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64598 AN: 151962 Hom.: 14231 Cov.: 35

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.403

GnomAD4 exome AF: 0.455 AC: 193700 AN: 425866 Hom.: 45242 Cov.: 4 AF XY: 0.449 AC XY: 101295 AN XY: 225406

African (AFR) AF: 0.311 AC: 2783 AN: 8960

American (AMR) AF: 0.541 AC: 7444 AN: 13754

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 5384 AN: 13048

East Asian (EAS) AF: 0.335 AC: 8998 AN: 26858

South Asian (SAS) AF: 0.363 AC: 15097 AN: 41576

European-Finnish (FIN) AF: 0.497 AC: 14797 AN: 29780

Middle Eastern (MID) AF: 0.305 AC: 604 AN: 1978

European-Non Finnish (NFE) AF: 0.482 AC: 127565 AN: 264880

Other (OTH) AF: 0.441 AC: 11028 AN: 25032

GnomAD4 genome AF: 0.425 AC: 64651 AN: 152080 Hom.: 14246 Cov.: 35 AF XY: 0.423 AC XY: 31419 AN XY: 74334

African (AFR) AF: 0.316 AC: 13115 AN: 41518

American (AMR) AF: 0.502 AC: 7672 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1417 AN: 3464

East Asian (EAS) AF: 0.328 AC: 1686 AN: 5144

South Asian (SAS) AF: 0.374 AC: 1809 AN: 4834

European-Finnish (FIN) AF: 0.483 AC: 5113 AN: 10592

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32388 AN: 67914

Other (OTH) AF: 0.405 AC: 855 AN: 2112

Alfa AF: 0.457 Hom.: 2624

Bravo AF: 0.421

Asia WGS AF: 0.413 AC: 1437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.015
DANN	Benign	0.34
PhyloP100		-4.5
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: rs3812550; hg19: chr9-139252879;