rs2869577

Positions:

• chr17-65199474-C-G

Variant summary

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

The NM_003835.4(RGS9):​c.976+2233C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 147,140 control chromosomes in the GnomAD database, including 2,192 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 0.12 (2192 hom., cov: 31)
• Consequence: RGS9 NM_003835.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

Genes affected

RGS9 (HGNC:10004): (regulator of G protein signaling 9) This gene encodes a member of the RGS family of GTPase activating proteins that function in various signaling pathways by accelerating the deactivation of G proteins. This protein is anchored to photoreceptor membranes in retinal cells and deactivates G proteins in the rod and cone phototransduction cascades. Mutations in this gene result in bradyopsia. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Sep 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RGS9	NM_003835.4	c.976+2233C>G		intron_variant		ENST00000262406.10	NP_003826.2
RGS9	NM_001081955.3	c.967+2233C>G		intron_variant			NP_001075424.1
RGS9	NM_001165933.2	c.967+2233C>G		intron_variant			NP_001159405.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RGS9	ENST00000262406.10	c.976+2233C>G		intron_variant		1	NM_003835.4	ENSP00000262406	P4

Frequencies

GnomAD3 genomes AF: 0.120 AC: 17684 AN: 147074 Hom.: 2189 Cov.: 31

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.0342

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.0231

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.0760

Gnomad FIN AF: 0.0286

Gnomad MID AF: 0.0774

Gnomad NFE AF: 0.0204

Gnomad OTH AF: 0.0884

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

GnomAD4 genome AF: 0.120 AC: 17716 AN: 147140 Hom.: 2192 Cov.: 31 AF XY: 0.124 AC XY: 8888 AN XY: 71550

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.0231

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.0756

Gnomad4 FIN AF: 0.0286

Gnomad4 NFE AF: 0.0204

Gnomad4 OTH AF: 0.0914

Alfa AF: 0.0790 Hom.: 163

Bravo AF: 0.146

Asia WGS AF: 0.225 AC: 779 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.74
DANN	Benign	0.46

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

Other links and lift over

dbSNP: rs2869577; hg19: chr17-63195592;