1-163137317-T-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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]

RGS5 Gene-Disease associations (from GenCC):

• essential hypertension, genetic

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000469495.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RGS5	ENST00000469495.5	TSL:5	n.167+15233A>C		intron	N/A

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

African (AFR) AF: 0.181 AC: 7490 AN: 41486

American (AMR) AF: 0.365 AC: 5579 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1106 AN: 3470

East Asian (EAS) AF: 0.281 AC: 1453 AN: 5166

South Asian (SAS) AF: 0.339 AC: 1634 AN: 4820

European-Finnish (FIN) AF: 0.378 AC: 3991 AN: 10552

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19311 AN: 67972

Other (OTH) AF: 0.300 AC: 634 AN: 2110

Alfa AF: 0.282 Hom.: 25523

Bravo AF: 0.265

Asia WGS AF: 0.305 AC: 1060 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	11
DANN	Benign	0.84
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs10494382; hg19: chr1-163107107;