XM_017021825.3:c.1423-26033T>C

Variant names:

• chr14-72603947-T-C
• rs7160623
• XM_017021825.3:c.1423-26033T>C

Variant summary

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

The XM_017021825.3(RGS6):​c.1423-26033T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 151,990 control chromosomes in the GnomAD database, including 14,332 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 0.41 (14332 hom., cov: 32)
• Consequence: RGS6 XM_017021825.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0340
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62888 AN: 151872 Hom.: 14333 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.414 AC: 62902 AN: 151990 Hom.: 14332 Cov.: 32 AF XY: 0.418 AC XY: 31051 AN XY: 74252

African (AFR) AF: 0.237 AC: 9828 AN: 41456

American (AMR) AF: 0.401 AC: 6136 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2074 AN: 3472

East Asian (EAS) AF: 0.762 AC: 3931 AN: 5160

South Asian (SAS) AF: 0.468 AC: 2255 AN: 4814

European-Finnish (FIN) AF: 0.440 AC: 4630 AN: 10522

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32425 AN: 67964

Other (OTH) AF: 0.465 AC: 980 AN: 2106

Alfa AF: 0.457 Hom.: 12743

Bravo AF: 0.404

Asia WGS AF: 0.580 AC: 2017 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7
DANN	Benign	0.75
PhyloP100		0.034

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7160623; hg19: chr14-73070655;