rs2349433

chr6-153062620-A-Gchr6-153062620-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012419.5(RGS17):c.-25-18577T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 151,980 control chromosomes in the GnomAD database, including 11,921 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 0.38 (11921 hom., cov: 31)
• Consequence: RGS17 NM_012419.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RGS17	NM_012419.5	c.-25-18577T>C		intron_variant		ENST00000206262.2
RGS17	XM_047418634.1	c.21-18577T>C		intron_variant
RGS17	XM_047418635.1	c.9-18577T>C		intron_variant
RGS17	XM_047418636.1	c.-25-18577T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RGS17	ENST00000206262.2	c.-25-18577T>C		intron_variant		1	NM_012419.5	P1

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58321 AN: 151860 Hom.: 11896 Cov.: 31

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.384 AC: 58395 AN: 151980 Hom.: 11921 Cov.: 31 AF XY: 0.389 AC XY: 28881 AN XY: 74280

Gnomad4 AFR AF: 0.495

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.622

Gnomad4 SAS AF: 0.509

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.366

Alfa AF: 0.329 Hom.: 2320

Bravo AF: 0.389

Asia WGS AF: 0.510 AC: 1772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	2.3
Dann	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2349433; hg19: chr6-153383755;