14-72024298-T-C

Variant names:

• chr14-72024298-T-C
• rs6574039
• NM_001204424.2:c.84+59423T>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.84+59423T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.778 in 152,110 control chromosomes in the GnomAD database, including 46,639 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 (46639 hom., cov: 31)
• Consequence: RGS6 NM_001204424.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29
• 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=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RGS6	NM_001204424.2	c.84+59423T>C		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.84+59423T>C		intron_variant	Intron 2 of 17	2	NM_001204424.2	ENSP00000451030.1

Frequencies

GnomAD3 genomes AF: 0.778 AC: 118276 AN: 151990 Hom.: 46621 Cov.: 31

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.889

Gnomad FIN AF: 0.916

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.772

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

GnomAD4 genome AF: 0.778 AC: 118341 AN: 152110 Hom.: 46639 Cov.: 31 AF XY: 0.785 AC XY: 58424 AN XY: 74386

African (AFR) AF: 0.640 AC: 26531 AN: 41458

American (AMR) AF: 0.824 AC: 12583 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.787 AC: 2729 AN: 3466

East Asian (EAS) AF: 0.815 AC: 4214 AN: 5172

South Asian (SAS) AF: 0.890 AC: 4288 AN: 4818

European-Finnish (FIN) AF: 0.916 AC: 9716 AN: 10612

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.818 AC: 55618 AN: 67990

Other (OTH) AF: 0.772 AC: 1632 AN: 2114

Alfa AF: 0.761 Hom.: 5517

Bravo AF: 0.766

Asia WGS AF: 0.839 AC: 2916 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.9
DANN	Benign	0.65
PhyloP100		1.3
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: rs6574039; hg19: chr14-72491015;