chr14-72345817-A-G

Variant names:

• chr14-72345817-A-G
• rs2681735
• NM_001204424.2:c.85-6278A>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.85-6278A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 152,128 control chromosomes in the GnomAD database, including 15,957 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 0.45 (15957 hom., cov: 33)
• Consequence: RGS6 NM_001204424.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25
• 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=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.557 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RGS6	NM_001204424.2	MANE Select	c.85-6278A>G		intron	N/A	NP_001191353.1
	RGS6	NM_001370275.1		c.85-6278A>G		intron	N/A	NP_001357204.1
	RGS6	NM_001370276.1		c.85-6278A>G		intron	N/A	NP_001357205.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RGS6	ENST00000553525.6	TSL:2 MANE Select	c.85-6278A>G		intron	N/A	ENSP00000451030.1
	RGS6	ENST00000556437.5	TSL:1	c.85-6278A>G		intron	N/A	ENSP00000451855.1
	RGS6	ENST00000404301.6	TSL:1	c.85-6278A>G		intron	N/A	ENSP00000385243.2

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68915 AN: 152008 Hom.: 15929 Cov.: 33

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.454 AC: 69000 AN: 152128 Hom.: 15957 Cov.: 33 AF XY: 0.459 AC XY: 34160 AN XY: 74382

African (AFR) AF: 0.536 AC: 22227 AN: 41496

American (AMR) AF: 0.460 AC: 7028 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1290 AN: 3472

East Asian (EAS) AF: 0.339 AC: 1754 AN: 5176

South Asian (SAS) AF: 0.575 AC: 2775 AN: 4826

European-Finnish (FIN) AF: 0.467 AC: 4947 AN: 10590

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27522 AN: 67970

Other (OTH) AF: 0.439 AC: 927 AN: 2110

Alfa AF: 0.432 Hom.: 4284

Bravo AF: 0.453

Asia WGS AF: 0.495 AC: 1722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.6
DANN	Benign	0.20
PhyloP100		1.2
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: rs2681735; hg19: chr14-72812525;