rs3009907

Variant names:

• chr10-119502942-G-T
• rs3009907
• NM_001005339.2:c.400-2683C>A

Variant summary

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

The NM_001005339.2(RGS10):​c.400-2683C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,134 control chromosomes in the GnomAD database, including 1,558 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 0.13 (1558 hom., cov: 31)
• Consequence: RGS10 NM_001005339.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.153
• Publications: 2 publications found

Genes affected

RGS10 (HGNC:9992): (regulator of G protein signaling 10) Regulator of G protein signaling (RGS) family members are regulatory molecules that act as GTPase activating proteins (GAPs) for G alpha subunits of heterotrimeric G proteins. RGS proteins are able to deactivate G protein subunits of the Gi alpha, Go alpha and Gq alpha subtypes. They drive G proteins into their inactive GDP-bound forms. Regulator of G protein signaling 10 belongs to this family. All RGS proteins share a conserved 120-amino acid sequence termed the RGS domain. This protein associates specifically with the activated forms of the two related G-protein subunits, G-alphai3 and G-alphaz but fails to interact with the structurally and functionally distinct G-alpha subunits. Regulator of G protein signaling 10 protein is localized in the nucleus. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001005339.2. 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
	RGS10	NM_001005339.2	MANE Select	c.400-2683C>A		intron	N/A	NP_001005339.1
	RGS10	NM_002925.4		c.358-2683C>A		intron	N/A	NP_002916.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RGS10	ENST00000369103.3	TSL:1 MANE Select	c.400-2683C>A		intron	N/A	ENSP00000358099.2
	RGS10	ENST00000369101.7	TSL:1	c.376-2683C>A		intron	N/A	ENSP00000358097.3
	RGS10	ENST00000392865.5	TSL:1	c.358-2683C>A		intron	N/A	ENSP00000376605.1

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19245 AN: 152016 Hom.: 1555 Cov.: 31

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.0571

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0227

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0946

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.127 AC: 19268 AN: 152134 Hom.: 1558 Cov.: 31 AF XY: 0.124 AC XY: 9238 AN XY: 74356

African (AFR) AF: 0.198 AC: 8215 AN: 41496

American (AMR) AF: 0.115 AC: 1753 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 402 AN: 3466

East Asian (EAS) AF: 0.253 AC: 1306 AN: 5152

South Asian (SAS) AF: 0.118 AC: 570 AN: 4824

European-Finnish (FIN) AF: 0.0227 AC: 241 AN: 10610

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0946 AC: 6434 AN: 67978

Other (OTH) AF: 0.125 AC: 265 AN: 2116

Alfa AF: 0.108 Hom.: 3744

Bravo AF: 0.139

Asia WGS AF: 0.157 AC: 546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.3
DANN	Benign	0.92
PhyloP100		0.15
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: rs3009907; hg19: chr10-121262454;