rs2239266

Positions:

• chr14-72010015-G-A

Variant summary

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

The NM_001204424.2(RGS6):​c.84+45140G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0751 in 152,238 control chromosomes in the GnomAD database, including 992 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 0.075 (992 hom., cov: 33)
• Consequence: RGS6 NM_001204424.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.557

Genes affected

RGS6 (HGNC:10002): (regulator of G protein signaling 6) This gene encodes a member of the RGS (regulator of G protein signaling) family of proteins, which are defined by the presence of a RGS domain that confers the GTPase-activating activity of these proteins toward certain G alpha subunits. This protein also belongs to a subfamily of RGS proteins characterized by the presence of DEP and GGL domains, the latter a G beta 5-interacting domain. The RGS proteins negatively regulate G protein signaling, and may modulate neuronal, cardiovascular, lymphocytic activities, and cancer risk. Many alternatively spliced transcript variants encoding different isoforms with long or short N-terminal domains, complete or incomplete GGL domains, and distinct C-terminal domains, have been described for this gene, however, the full-length nature of some of these variants is not known.[provided by RefSeq, Mar 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RGS6	NM_001204424.2	c.84+45140G>A		intron_variant		ENST00000553525.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RGS6	ENST00000553525.6	c.84+45140G>A		intron_variant		2	NM_001204424.2	P1

Frequencies

GnomAD3 genomes AF: 0.0750 AC: 11411 AN: 152120 Hom.: 993 Cov.: 33

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.0765

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.0663

Gnomad FIN AF: 0.0412

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00878

Gnomad OTH AF: 0.0516

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

GnomAD4 genome AF: 0.0751 AC: 11428 AN: 152238 Hom.: 992 Cov.: 33 AF XY: 0.0773 AC XY: 5754 AN XY: 74444

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.0766

Gnomad4 ASJ AF: 0.00202

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.0655

Gnomad4 FIN AF: 0.0412

Gnomad4 NFE AF: 0.00878

Gnomad4 OTH AF: 0.0516

Alfa AF: 0.0242 Hom.: 352

Bravo AF: 0.0834

Asia WGS AF: 0.126 AC: 440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.0
DANN	Benign	0.66

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: rs2239266; hg19: chr14-72476732;