rs1384797

Positions:

• chr8-53881368-T-C

Variant summary

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

The ENST00000297313.8(RGS20):​c.510+1766T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 151,930 control chromosomes in the GnomAD database, including 3,682 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 0.15 (3682 hom., cov: 31)
• Consequence: RGS20 ENST00000297313.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RGS20	NM_170587.4	c.510+1766T>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+1766T>C		intron_variant		1	NM_170587.4	ENSP00000297313

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22446 AN: 151810 Hom.: 3645 Cov.: 31

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0952

Gnomad ASJ AF: 0.0375

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.0453

Gnomad MID AF: 0.0605

Gnomad NFE AF: 0.0192

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.148 AC: 22542 AN: 151930 Hom.: 3682 Cov.: 31 AF XY: 0.151 AC XY: 11242 AN XY: 74290

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.0954

Gnomad4 ASJ AF: 0.0375

Gnomad4 EAS AF: 0.322

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.0453

Gnomad4 NFE AF: 0.0192

Gnomad4 OTH AF: 0.126

Alfa AF: 0.0933 Hom.: 334

Bravo AF: 0.158

Asia WGS AF: 0.291 AC: 1012 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.8
DANN	Benign	0.23

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: rs1384797; hg19: chr8-54793928;