Variant rs2295230 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_012419.5(RGS17):c.54T>G(p.Ala18=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 1,610,784 control chromosomes in the GnomAD database, including 95,162 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 0.40 ( 13221 hom., cov: 32)

Exomes 𝑓: 0.32 ( 81941 hom. )

Consequence

RGS17
NM_012419.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.18

Variant links:

Genes affected

RGS17 (HGNC:14088): (regulator of G protein signaling 17) This gene encodes a member of the regulator of G-protein signaling family. This protein contains a conserved, 120 amino acid motif called the RGS domain and a cysteine-rich region. The protein attenuates the signaling activity of G-proteins by binding to activated, GTP-bound G alpha subunits and acting as a GTPase activating protein (GAP), increasing the rate of conversion of the GTP to GDP. This hydrolysis allows the G alpha subunits to bind G beta/gamma subunit heterodimers, forming inactive G-protein heterotrimers, thereby terminating the signal. [provided by RefSeq, Jul 2008]

RGS17 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BP7

Synonymous conserved (PhyloP=-1.17 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
RGS17	NM_012419.5 linkuse as main transcript	c.54T>G	p.Ala18=	synonymous_variant	2/5	ENST00000206262.2	NP_036551.3
RGS17	XM_047418634.1 linkuse as main transcript	c.99T>G	p.Ala33=	synonymous_variant	2/5		XP_047274590.1
RGS17	XM_047418635.1 linkuse as main transcript	c.87T>G	p.Ala29=	synonymous_variant	2/5		XP_047274591.1
RGS17	XM_047418636.1 linkuse as main transcript	c.54T>G	p.Ala18=	synonymous_variant	2/5		XP_047274592.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RGS17	ENST00000206262.2 linkuse as main transcript	c.54T>G	p.Ala18=	synonymous_variant	2/5	1	NM_012419.5	ENSP00000206262	P1
RGS17	ENST00000367225.6 linkuse as main transcript	c.54T>G	p.Ala18=	synonymous_variant	1/4	1		ENSP00000356194	P1

Frequencies

GnomAD3 genomes

AF:

0.401

AC:

60820

AN:

151814

Hom.:

13197

Cov.:

show subpopulations

Gnomad AFR

AF:

0.557

Gnomad AMI

AF:

0.195

Gnomad AMR

AF:

0.390

Gnomad ASJ

AF:

0.330

Gnomad EAS

AF:

0.620

Gnomad SAS

AF:

0.501

Gnomad FIN

AF:

0.349

Gnomad MID

AF:

0.389

Gnomad NFE

AF:

0.299

Gnomad OTH

AF:

0.377

GnomAD3 exomes

AF:

0.384

AC:

95916

AN:

249666

Hom.:

20079

AF XY:

0.380

AC XY:

51315

AN XY:

135030

show subpopulations

Gnomad AFR exome

AF:

0.561

Gnomad AMR exome

AF:

0.438

Gnomad ASJ exome

AF:

0.317

Gnomad EAS exome

AF:

0.626

Gnomad SAS exome

AF:

0.486

Gnomad FIN exome

AF:

0.337

Gnomad NFE exome

AF:

0.294

Gnomad OTH exome

AF:

0.342

GnomAD4 exome

AF:

0.323

AC:

471383

AN:

1458850

Hom.:

81941

Cov.:

AF XY:

0.327

AC XY:

237470

AN XY:

725854

show subpopulations

Gnomad4 AFR exome

AF:

0.572

Gnomad4 AMR exome

AF:

0.430

Gnomad4 ASJ exome

AF:

0.313

Gnomad4 EAS exome

AF:

0.594

Gnomad4 SAS exome

AF:

0.483

Gnomad4 FIN exome

AF:

0.338

Gnomad4 NFE exome

AF:

0.287

Gnomad4 OTH exome

AF:

0.349

GnomAD4 genome

AF:

0.401

AC:

60892

AN:

151934

Hom.:

13221

Cov.:

AF XY:

0.405

AC XY:

30059

AN XY:

74246

show subpopulations

Gnomad4 AFR

AF:

0.557

Gnomad4 AMR

AF:

0.390

Gnomad4 ASJ

AF:

0.330

Gnomad4 EAS

AF:

0.620

Gnomad4 SAS

AF:

0.503

Gnomad4 FIN

AF:

0.349

Gnomad4 NFE

AF:

0.299

Gnomad4 OTH

AF:

0.375

Alfa

AF:

0.297

Hom.:

2981

Bravo

AF:

0.408

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.051

DANN

Benign

0.29

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over