rs860195

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.973
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons MANE Protein UniProt
RGS6NM_001204424.2 linkc.85-47745A>G intron_variant ENST00000553525.6 NP_001191353.1 P49758-3Q2M3K2B7Z2A0

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RGS6ENST00000553525.6 linkc.85-47745A>G intron_variant 2 NM_001204424.2 ENSP00000451030.1 P49758-3

Frequencies

GnomAD3 genomes
AF:
0.604
AC:
91836
AN:
151968
Hom.:
28380
Cov.:
32
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.732
Gnomad4 AMR
AF:
0.600
Gnomad4 ASJ
AF:
0.540
Gnomad4 EAS
AF:
0.655
Gnomad4 SAS
AF:
0.639
Gnomad4 FIN
AF:
0.546
Gnomad4 NFE
AF:
0.534
Gnomad4 OTH
AF:
0.611
Alfa
AF:
0.428
Hom.:
1139
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

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs860195; hg19: chr14-72771058; API