chr14-72304350-A-G

Variant names:

• chr14-72304350-A-G
• rs860195
• NM_001204424.2:c.85-47745A>G

Variant summary

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

The NM_001204424.2(RGS6):​c.85-47745A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.605 in 152,086 control chromosomes in the GnomAD database, including 28,432 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 0.60 (28432 hom., cov: 32)
• Consequence: RGS6 NM_001204424.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.973
• Publications: 4 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RGS6	NM_001204424.2	c.85-47745A>G		intron_variant	Intron 2 of 17	ENST00000553525.6	NP_001191353.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RGS6	ENST00000553525.6	c.85-47745A>G		intron_variant	Intron 2 of 17	2	NM_001204424.2	ENSP00000451030.1

Frequencies

GnomAD3 genomes AF: 0.604 AC: 91836 AN: 151968 Hom.: 28380 Cov.: 32

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.655

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.605 AC: 91952 AN: 152086 Hom.: 28432 Cov.: 32 AF XY: 0.606 AC XY: 45005 AN XY: 74326

African (AFR) AF: 0.732 AC: 30359 AN: 41498

American (AMR) AF: 0.600 AC: 9164 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1876 AN: 3472

East Asian (EAS) AF: 0.655 AC: 3388 AN: 5172

South Asian (SAS) AF: 0.639 AC: 3074 AN: 4808

European-Finnish (FIN) AF: 0.546 AC: 5756 AN: 10548

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.534 AC: 36310 AN: 67984

Other (OTH) AF: 0.611 AC: 1291 AN: 2114

Alfa AF: 0.597 Hom.: 4840

Bravo AF: 0.611

Asia WGS AF: 0.655 AC: 2279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.21
DANN	Benign	0.40
PhyloP100		-0.97
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: rs860195; hg19: chr14-72771058;