rs10494382

Variant names:

• chr1-163137317-T-G
• rs10494382
• ENST00000469495.5:n.167+15233A>C

Variant summary

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

The ENST00000469495.5(RGS5):​n.167+15233A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 152,050 control chromosomes in the GnomAD database, including 6,024 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 0.27 (6024 hom., cov: 32)
• Consequence: RGS5 ENST00000469495.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220

Genes affected

RGS5 (HGNC:10001): (regulator of G protein signaling 5) This locus represents naturally occurring readthrough transcription between the neighboring LOC127814295 (uncharacterized LOC127814295) and RGS5 (regulator of G-protein signaling 5) genes on chromosome 1. Some variants of the readthrough transcript encode novel proteins with unique N-termini. [provided by RefSeq, Nov 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RGS5	ENST00000469495.5	n.167+15233A>C		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41493 AN: 151930 Hom.: 6018 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.273 AC: 41517 AN: 152050 Hom.: 6024 Cov.: 32 AF XY: 0.280 AC XY: 20829 AN XY: 74314

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.378

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.300

Alfa AF: 0.288 Hom.: 12486

Bravo AF: 0.265

Asia WGS AF: 0.305 AC: 1060 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	11
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10494382; hg19: chr1-163107107;