rs10799902

Variant names:

• chr1-163189892-A-G
• rs10799902
• NM_003617.4:c.44+12900T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003617.4(RGS5):​c.44+12900T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 152,070 control chromosomes in the GnomAD database, including 26,847 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 0.58 (26847 hom., cov: 31)
• Consequence: RGS5 NM_003617.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 1 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-AS1 (HGNC:40504): (RGS5 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003617.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RGS5	NM_003617.4	MANE Select	c.44+12900T>C		intron	N/A	NP_003608.1	O15539-1
	RGS5	NM_001414472.1		c.66-21524T>C		intron	N/A	NP_001401401.1
	RGS5	NM_001414473.1		c.66-21524T>C		intron	N/A	NP_001401402.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RGS5	ENST00000313961.10	TSL:1 MANE Select	c.44+12900T>C		intron	N/A	ENSP00000319308.5	O15539-1
	RGS5	ENST00000527988.1	TSL:1	c.-108+12900T>C		intron	N/A	ENSP00000432313.1	O15539-2
	RGS5	ENST00000367903.7	TSL:3	c.70-17300T>C		intron	N/A	ENSP00000356879.3	B1APM2

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87831 AN: 151952 Hom.: 26836 Cov.: 31

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.578 AC: 87885 AN: 152070 Hom.: 26847 Cov.: 31 AF XY: 0.579 AC XY: 43067 AN XY: 74330

African (AFR) AF: 0.355 AC: 14731 AN: 41474

American (AMR) AF: 0.659 AC: 10076 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.624 AC: 2165 AN: 3470

East Asian (EAS) AF: 0.719 AC: 3712 AN: 5160

South Asian (SAS) AF: 0.642 AC: 3098 AN: 4824

European-Finnish (FIN) AF: 0.649 AC: 6859 AN: 10564

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.664 AC: 45149 AN: 67964

Other (OTH) AF: 0.604 AC: 1279 AN: 2116

Alfa AF: 0.643 Hom.: 53350

Bravo AF: 0.574

Asia WGS AF: 0.622 AC: 2163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.52
PhyloP100		0.35
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10799902; hg19: chr1-163159682;