rs2220093

Positions:

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

Variant summary

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

The NM_170587.4(RGS20):​c.510+9165T>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_170587.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

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]

RGS20 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RGS20	NM_170587.4	c.510+9165T>C		intron_variant		ENST00000297313.8	NP_733466.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RGS20	ENST00000297313.8	c.510+9165T>C		intron_variant		1	NM_170587.4	ENSP00000297313.3
RGS20	ENST00000276500.4	c.69+7683T>C		intron_variant		1		ENSP00000276500.4

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

Gnomad4 AFR AF: 0.624

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.0925

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.256

Alfa AF: 0.134 Hom.: 2861

Bravo AF: 0.299

Asia WGS AF: 0.332 AC: 1151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs2220093; hg19: chr8-54801327;