chr9-113597059-T-C

Position:

• chr9-113597059-T-C

Variant summary

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

The NM_001394167.1(RGS3):​c.*106T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.776 in 935,266 control chromosomes in the GnomAD database, including 283,653 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 0.78 (46949 hom., cov: 32)
  • Exomes 𝑓: 0.77 (236704 hom.)
• Consequence: RGS3 NM_001394167.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.149

Genes affected

RGS3 (HGNC:9999): (regulator of G protein signaling 3) This gene encodes a member of the regulator of G-protein signaling (RGS) family. This protein is a GTPase-activating protein that inhibits G-protein-mediated signal transduction. Alternative splicing and the use of alternative promoters results in multiple transcript variants encoding different isoforms. Long isoforms are largely cytosolic and plasma membrane-associated with a function in Wnt signaling and in the epithelial mesenchymal transition, while shorter N-terminally-truncated isoforms can be nuclear. [provided by RefSeq, Jan 2013]

RGS3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RGS3	NM_001394167.1	c.*106T>C		3_prime_UTR_variant	23/23	ENST00000695401.1	NP_001381096.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RGS3	ENST00000695401.1	c.*106T>C		3_prime_UTR_variant	23/23		NM_001394167.1	ENSP00000511882.1

Frequencies

GnomAD3 genomes AF: 0.784 AC: 119207 AN: 151970 Hom.: 46928 Cov.: 32

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.838

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.843

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.800

GnomAD4 exome AF: 0.775 AC: 606623 AN: 783178 Hom.: 236704 Cov.: 10 AF XY: 0.778 AC XY: 311804 AN XY: 401024

Gnomad4 AFR exome AF: 0.795

Gnomad4 AMR exome AF: 0.879

Gnomad4 ASJ exome AF: 0.811

Gnomad4 EAS exome AF: 0.984

Gnomad4 SAS exome AF: 0.843

Gnomad4 FIN exome AF: 0.740

Gnomad4 NFE exome AF: 0.749

Gnomad4 OTH exome AF: 0.787

GnomAD4 genome AF: 0.784 AC: 119272 AN: 152088 Hom.: 46949 Cov.: 32 AF XY: 0.788 AC XY: 58628 AN XY: 74364

Gnomad4 AFR AF: 0.794

Gnomad4 AMR AF: 0.838

Gnomad4 ASJ AF: 0.787

Gnomad4 EAS AF: 0.988

Gnomad4 SAS AF: 0.843

Gnomad4 FIN AF: 0.747

Gnomad4 NFE AF: 0.750

Gnomad4 OTH AF: 0.803

Alfa AF: 0.768 Hom.: 19842

Bravo AF: 0.794

Asia WGS AF: 0.900 AC: 3130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	15
DANN	Benign	0.80

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: rs1051013; hg19: chr9-116359339;