rs6574074

Variant names:

• chr14-72408978-G-C
• rs6574074
• NM_001204424.2:c.185-45550G>C

Variant summary

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

The NM_001204424.2(RGS6):​c.185-45550G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 151,944 control chromosomes in the GnomAD database, including 17,680 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 0.47 (17680 hom., cov: 32)
• Consequence: RGS6 NM_001204424.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157
• Publications: 0 publications found

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]

LOC105370559 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001204424.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RGS6	NM_001204424.2	MANE Select	c.185-45550G>C		intron	N/A	NP_001191353.1	P49758-3
	RGS6	NM_001370275.1		c.185-45550G>C		intron	N/A	NP_001357204.1
	RGS6	NM_001370276.1		c.185-45550G>C		intron	N/A	NP_001357205.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RGS6	ENST00000553525.6	TSL:2 MANE Select	c.185-45550G>C		intron	N/A	ENSP00000451030.1	P49758-3
	RGS6	ENST00000556437.5	TSL:1	c.185-45550G>C		intron	N/A	ENSP00000451855.1	P49758-3
	RGS6	ENST00000404301.6	TSL:1	c.185-45550G>C		intron	N/A	ENSP00000385243.2	P49758-15

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71790 AN: 151824 Hom.: 17630 Cov.: 32

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.473 AC: 71907 AN: 151944 Hom.: 17680 Cov.: 32 AF XY: 0.476 AC XY: 35331 AN XY: 74254

African (AFR) AF: 0.586 AC: 24315 AN: 41472

American (AMR) AF: 0.464 AC: 7084 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1182 AN: 3468

East Asian (EAS) AF: 0.613 AC: 3160 AN: 5152

South Asian (SAS) AF: 0.516 AC: 2486 AN: 4816

European-Finnish (FIN) AF: 0.499 AC: 5265 AN: 10548

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.397 AC: 26971 AN: 67918

Other (OTH) AF: 0.460 AC: 971 AN: 2112

Alfa AF: 0.441 Hom.: 1891

Bravo AF: 0.472

Asia WGS AF: 0.593 AC: 2059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.75
PhyloP100		-0.16
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: rs6574074; hg19: chr14-72875686;