1-192400980-T-C

Variant names:

• chr1-192400980-T-C
• rs2369810
• ENST00000642855.1:n.860-13166A>G

Variant summary

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

The ENST00000642855.1(RGS2-AS1):​n.860-13166A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.9 in 151,846 control chromosomes in the GnomAD database, including 61,626 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 0.90 (61626 hom., cov: 32)
• Consequence: RGS2-AS1 ENST00000642855.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.257
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.93 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.860-13166A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.900 AC: 136523 AN: 151728 Hom.: 61602 Cov.: 32

Gnomad AFR AF: 0.843

Gnomad AMI AF: 0.929

Gnomad AMR AF: 0.887

Gnomad ASJ AF: 0.948

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.929

Gnomad FIN AF: 0.892

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.936

Gnomad OTH AF: 0.903

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

GnomAD4 genome AF: 0.900 AC: 136602 AN: 151846 Hom.: 61626 Cov.: 32 AF XY: 0.897 AC XY: 66572 AN XY: 74214

African (AFR) AF: 0.843 AC: 34916 AN: 41436

American (AMR) AF: 0.886 AC: 13471 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.948 AC: 3286 AN: 3468

East Asian (EAS) AF: 0.869 AC: 4469 AN: 5144

South Asian (SAS) AF: 0.928 AC: 4479 AN: 4826

European-Finnish (FIN) AF: 0.892 AC: 9470 AN: 10612

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.936 AC: 63480 AN: 67848

Other (OTH) AF: 0.904 AC: 1906 AN: 2108

Alfa AF: 0.929 Hom.: 107945

Bravo AF: 0.897

Asia WGS AF: 0.884 AC: 3075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.1
DANN	Benign	0.67
PhyloP100		-0.26

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: rs2369810;

hg19: chr1-192370110;