rs2220093

Variant names:

• chr8-53888767-T-C
• rs2220093
• NM_003702.5:c.69+7683T>C

Your query was ambiguous. Multiple possible variants found:

• chr8-53888767-T-C
• chr8-53888767-T-G

Variant summary

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

The NM_003702.5(RGS20):​c.69+7683T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 152,158 control chromosomes in the GnomAD database, including 9,751 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 0.28 (9751 hom., cov: 32)
• Consequence: RGS20 NM_003702.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 8 publications found

Genes affected

RGS20 (HGNC:14600): (regulator of G protein signaling 20) The protein encoded by this gene belongs to the family of regulator of G protein signaling (RGS) proteins, which are regulatory and structural components of G protein-coupled receptor complexes. RGS proteins inhibit signal transduction by increasing the GTPase activity of G protein alpha subunits, thereby driving them into their inactive GDP-bound forms. This protein selectively binds to G(z)-alpha and G(alpha)-i2 subunits, and regulates their signaling activities. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003702.5. 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
	RGS20	NM_003702.5	MANE Select	c.69+7683T>C		intron	N/A	NP_003693.2
	RGS20	NM_170587.4		c.510+9165T>C		intron	N/A	NP_733466.1	O76081-1
	RGS20	NM_001286673.2		c.165+36703T>C		intron	N/A	NP_001273602.1	O76081-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RGS20	ENST00000276500.5	TSL:1 MANE Select	c.69+7683T>C		intron	N/A	ENSP00000276500.4	O76081-6
	RGS20	ENST00000297313.8	TSL:1	c.510+9165T>C		intron	N/A	ENSP00000297313.3	O76081-1
	RGS20	ENST00000344277.10	TSL:1	c.165+36703T>C		intron	N/A	ENSP00000344630.6	O76081-2

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42489 AN: 152040 Hom.: 9715 Cov.: 32

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.0925

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.280 AC: 42596 AN: 152158 Hom.: 9751 Cov.: 32 AF XY: 0.281 AC XY: 20893 AN XY: 74416

African (AFR) AF: 0.624 AC: 25859 AN: 41470

American (AMR) AF: 0.239 AC: 3660 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0925 AC: 321 AN: 3472

East Asian (EAS) AF: 0.389 AC: 2009 AN: 5168

South Asian (SAS) AF: 0.273 AC: 1319 AN: 4828

European-Finnish (FIN) AF: 0.163 AC: 1728 AN: 10594

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7048 AN: 68012

Other (OTH) AF: 0.256 AC: 542 AN: 2116

Alfa AF: 0.156 Hom.: 5897

Bravo AF: 0.299

Asia WGS AF: 0.332 AC: 1151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.92
DANN	Benign	0.49
PhyloP100		-1.4
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2220093;

hg19: chr8-54801327;