rs6704162

Variant names:

• chr1-192445292-A-G
• rs6704162
• ENST00000642855.1:n.859+30747T>C

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+30747T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,100 control chromosomes in the GnomAD database, including 2,042 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 0.15 (2042 hom., cov: 32)
• Consequence: RGS2-AS1 ENST00000642855.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400
• Publications: 6 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=-0.65).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.338 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+30747T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23382 AN: 151982 Hom.: 2043 Cov.: 32

Gnomad AFR AF: 0.0751

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.154 AC: 23377 AN: 152100 Hom.: 2042 Cov.: 32 AF XY: 0.156 AC XY: 11611 AN XY: 74346

African (AFR) AF: 0.0750 AC: 3117 AN: 41542

American (AMR) AF: 0.159 AC: 2424 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 500 AN: 3470

East Asian (EAS) AF: 0.159 AC: 821 AN: 5156

South Asian (SAS) AF: 0.352 AC: 1696 AN: 4814

European-Finnish (FIN) AF: 0.180 AC: 1911 AN: 10588

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12350 AN: 67964

Other (OTH) AF: 0.157 AC: 331 AN: 2112

Alfa AF: 0.176 Hom.: 1606

Bravo AF: 0.144

Asia WGS AF: 0.261 AC: 907 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	2.9
DANN	Benign	0.84
PhyloP100		-0.040

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: rs6704162;

hg19: chr1-192414422;