rs2760524

Variant names:

• chr1-192561418-A-G
• rs2760524
• ENST00000434300.3:n.234+5729T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-192561418-A-G
• chr1-192561418-A-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.409+5729T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.861 in 152,146 control chromosomes in the GnomAD database, including 56,658 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 0.86 (56658 hom., cov: 31)
• Consequence: RGS2-AS1 ENST00000642855.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.36
• Publications: 26 publications found

Genes affected

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

LOC105371664 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.943 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	ENST00000434300.3	TSL:5	n.234+5729T>C		intron	N/A
	RGS2-AS1	ENST00000642855.1		n.409+5729T>C		intron	N/A
	RGS2-AS1	ENST00000644058.2		n.634+5729T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.861 AC: 130821 AN: 152028 Hom.: 56598 Cov.: 31

Gnomad AFR AF: 0.951

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.800

Gnomad SAS AF: 0.912

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.846

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

GnomAD4 genome AF: 0.861 AC: 130937 AN: 152146 Hom.: 56658 Cov.: 31 AF XY: 0.863 AC XY: 64174 AN XY: 74380

African (AFR) AF: 0.951 AC: 39466 AN: 41498

American (AMR) AF: 0.805 AC: 12306 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.861 AC: 2990 AN: 3472

East Asian (EAS) AF: 0.801 AC: 4152 AN: 5186

South Asian (SAS) AF: 0.913 AC: 4392 AN: 4812

European-Finnish (FIN) AF: 0.868 AC: 9185 AN: 10580

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.819 AC: 55663 AN: 67994

Other (OTH) AF: 0.841 AC: 1777 AN: 2112

Alfa AF: 0.845 Hom.: 9825

Bravo AF: 0.860

Asia WGS AF: 0.872 AC: 3034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.25
DANN	Benign	0.67
PhyloP100		-2.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2760524;

hg19: chr1-192530548;