rs2816316

Variant names:

• chr1-192567683-C-A
• rs2816316
• ENST00000434300.3:n.165-467G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-192567683-C-A
• chr1-192567683-C-G
• chr1-192567683-C-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.340-467G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.788 in 152,094 control chromosomes in the GnomAD database, including 47,510 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 0.79 (47510 hom., cov: 32)
• Consequence: RGS2-AS1 ENST00000642855.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.127
• Publications: 99 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=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.888 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.165-467G>T		intron	N/A
	RGS2-AS1	ENST00000642855.1		n.340-467G>T		intron	N/A
	RGS2-AS1	ENST00000644058.2		n.565-467G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.788 AC: 119810 AN: 151976 Hom.: 47485 Cov.: 32

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.860

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.910

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.792

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

GnomAD4 genome AF: 0.788 AC: 119877 AN: 152094 Hom.: 47510 Cov.: 32 AF XY: 0.794 AC XY: 58991 AN XY: 74338

African (AFR) AF: 0.705 AC: 29245 AN: 41492

American (AMR) AF: 0.776 AC: 11842 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.860 AC: 2982 AN: 3468

East Asian (EAS) AF: 0.792 AC: 4094 AN: 5166

South Asian (SAS) AF: 0.910 AC: 4392 AN: 4824

European-Finnish (FIN) AF: 0.868 AC: 9194 AN: 10588

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.816 AC: 55467 AN: 67984

Other (OTH) AF: 0.788 AC: 1661 AN: 2108

Alfa AF: 0.810 Hom.: 199272

Bravo AF: 0.778

Asia WGS AF: 0.854 AC: 2969 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	2.2
DANN	Benign	0.74
PhyloP100		0.13

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: rs2816316;

hg19: chr1-192536813;