rs10494665

Variant names:

• chr1-192475126-G-A
• rs10494665
• ENST00000642855.1:n.859+913C>T

Variant summary

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

The ENST00000642855.1(RGS2-AS1):​n.859+913C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0466 in 152,194 control chromosomes in the GnomAD database, including 182 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 0.047 (182 hom., cov: 32)
• Consequence: RGS2-AS1 ENST00000642855.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.89
• Publications: 3 publications found

Genes affected

RGS2-AS1 (HGNC:49018): (RSG2 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0867 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000642855.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RGS2-AS1	ENST00000642855.1		n.859+913C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0466 AC: 7083 AN: 152076 Hom.: 179 Cov.: 32

Gnomad AFR AF: 0.0273

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.0320

Gnomad ASJ AF: 0.0427

Gnomad EAS AF: 0.0936

Gnomad SAS AF: 0.0689

Gnomad FIN AF: 0.0889

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0491

Gnomad OTH AF: 0.0407

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

GnomAD4 genome AF: 0.0466 AC: 7086 AN: 152194 Hom.: 182 Cov.: 32 AF XY: 0.0478 AC XY: 3557 AN XY: 74406

African (AFR) AF: 0.0275 AC: 1141 AN: 41532

American (AMR) AF: 0.0319 AC: 488 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0427 AC: 148 AN: 3470

East Asian (EAS) AF: 0.0936 AC: 485 AN: 5182

South Asian (SAS) AF: 0.0685 AC: 330 AN: 4818

European-Finnish (FIN) AF: 0.0889 AC: 942 AN: 10594

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0491 AC: 3339 AN: 68000

Other (OTH) AF: 0.0403 AC: 85 AN: 2110

Alfa AF: 0.0479 Hom.: 60

Bravo AF: 0.0412

Asia WGS AF: 0.0810 AC: 280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.46
PhyloP100		1.9

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10494665; hg19: chr1-192444256;