1-192815708-T-C

Variant names:

• chr1-192815708-T-C
• rs1819741
• ENST00000644058.2:n.202-49514A>G

Variant summary

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

The ENST00000644058.2(RGS2-AS1):​n.202-49514A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 152,108 control chromosomes in the GnomAD database, including 5,823 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 0.27 (5823 hom., cov: 32)
• Consequence: RGS2-AS1 ENST00000644058.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.386
• Publications: 7 publications found

Genes affected

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

ENSG00000296334 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000644058.2. 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	ENST00000644058.2		n.202-49514A>G		intron	N/A
	RGS2-AS1	ENST00000644134.1		n.105-49514A>G		intron	N/A
	RGS2-AS1	ENST00000645822.1		n.199+11196A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41555 AN: 151988 Hom.: 5819 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.273 AC: 41569 AN: 152108 Hom.: 5823 Cov.: 32 AF XY: 0.274 AC XY: 20365 AN XY: 74350

African (AFR) AF: 0.267 AC: 11077 AN: 41472

American (AMR) AF: 0.251 AC: 3833 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1019 AN: 3472

East Asian (EAS) AF: 0.448 AC: 2320 AN: 5180

South Asian (SAS) AF: 0.292 AC: 1410 AN: 4826

European-Finnish (FIN) AF: 0.235 AC: 2489 AN: 10576

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18379 AN: 67988

Other (OTH) AF: 0.268 AC: 565 AN: 2112

Alfa AF: 0.244 Hom.: 2510

Bravo AF: 0.273

Asia WGS AF: 0.395 AC: 1370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.7
DANN	Benign	0.77
PhyloP100		0.39

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: rs1819741;

hg19: chr1-192784838;