rs10799902

Positions:

• chr1-163189892-A-G

Variant summary

Our verdict is Benign. Variant got -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

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RGS5	NM_003617.4	c.44+12900T>C		intron_variant		ENST00000313961.10
RGS5-AS1	NR_110699.1	n.259-16805A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RGS5	ENST00000313961.10	c.44+12900T>C		intron_variant		1	NM_003617.4	P4
RGS5-AS1	ENST00000415437.1	n.259-16805A>G		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.659

Gnomad4 ASJ AF: 0.624

Gnomad4 EAS AF: 0.719

Gnomad4 SAS AF: 0.642

Gnomad4 FIN AF: 0.649

Gnomad4 NFE AF: 0.664

Gnomad4 OTH AF: 0.604

Alfa AF: 0.651 Hom.: 42723

Bravo AF: 0.574

Asia WGS AF: 0.622 AC: 2163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.52

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: rs10799902; hg19: chr1-163159682;