rs2662774

Positions:

• chr1-163191230-G-A

Variant summary

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

The NM_003617.4(RGS5):​c.44+11562C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 151,996 control chromosomes in the GnomAD database, including 4,843 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 0.24 (4843 hom., cov: 32)
• Consequence: RGS5 NM_003617.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RGS5	NM_003617.4	c.44+11562C>T		intron_variant		ENST00000313961.10	NP_003608.1
RGS5-AS1	NR_110699.1	n.259-15467G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RGS5	ENST00000313961.10	c.44+11562C>T		intron_variant		1	NM_003617.4	ENSP00000319308	P4
RGS5-AS1	ENST00000415437.1	n.259-15467G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36731 AN: 151876 Hom.: 4849 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.242 AC: 36760 AN: 151996 Hom.: 4843 Cov.: 32 AF XY: 0.240 AC XY: 17855 AN XY: 74296

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.223

Alfa AF: 0.234 Hom.: 1536

Bravo AF: 0.243

Asia WGS AF: 0.169 AC: 585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.0
DANN	Benign	0.72

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: rs2662774; hg19: chr1-163161020;