rs10514869

chr17-65105140-A-G

Variant summary

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

The NR_110801.1(LOC100507002):n.321+3844A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0363 in 152,248 control chromosomes in the GnomAD database, including 578 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 0.036 (578 hom., cov: 32)
• Consequence: LOC100507002 NR_110801.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.550

Genes affected

LOC100507002 (HGNC:):

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100507002	NR_110801.1	n.321+3844A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RGS9	ENST00000635833.1	c.57+4098A>G		intron_variant		5		A2
RGS9	ENST00000582940.2	n.165+4098A>G		intron_variant, non_coding_transcript_variant		5
RGS9	ENST00000637818.1	n.303+3844A>G		intron_variant, non_coding_transcript_variant		5
RGS9	ENST00000638125.1	n.321+3844A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0364 AC: 5532 AN: 152130 Hom.: 579 Cov.: 32

Gnomad AFR AF: 0.00410

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0713

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.0511

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0131

Gnomad OTH AF: 0.0282

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

GnomAD4 genome AF: 0.0363 AC: 5527 AN: 152248 Hom.: 578 Cov.: 32 AF XY: 0.0427 AC XY: 3182 AN XY: 74446

Gnomad4 AFR AF: 0.00409

Gnomad4 AMR AF: 0.0714

Gnomad4 ASJ AF: 0.00317

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.0511

Gnomad4 NFE AF: 0.0131

Gnomad4 OTH AF: 0.0293

Alfa AF: 0.0199 Hom.: 17

Bravo AF: 0.0354

Asia WGS AF: 0.241 AC: 838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.49
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10514869; hg19: chr17-63101258;