rs16834831

Variant names:

• chr1-192790056-T-G
• rs16834831
• ENST00000644058.2:n.202-23862A>C

Variant summary

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

The ENST00000644058.2(RGS2-AS1):​n.202-23862A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0984 in 152,058 control chromosomes in the GnomAD database, including 954 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 0.098 (954 hom., cov: 32)
• Consequence: RGS2-AS1 ENST00000644058.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.49
• Publications: 3 publications found

Genes affected

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

LOC105371665 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.158 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.202-23862A>C		intron	N/A
	RGS2-AS1	ENST00000644134.1		n.105-23862A>C		intron	N/A
	RGS2-AS1	ENST00000645822.1		n.369+2243A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0984 AC: 14953 AN: 151940 Hom.: 952 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.0763

Gnomad SAS AF: 0.0436

Gnomad FIN AF: 0.0310

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0716

Gnomad OTH AF: 0.0986

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

GnomAD4 genome AF: 0.0984 AC: 14963 AN: 152058 Hom.: 954 Cov.: 32 AF XY: 0.0960 AC XY: 7135 AN XY: 74326

African (AFR) AF: 0.161 AC: 6674 AN: 41466

American (AMR) AF: 0.125 AC: 1906 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 347 AN: 3464

East Asian (EAS) AF: 0.0760 AC: 391 AN: 5142

South Asian (SAS) AF: 0.0438 AC: 211 AN: 4812

European-Finnish (FIN) AF: 0.0310 AC: 329 AN: 10598

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0715 AC: 4861 AN: 67978

Other (OTH) AF: 0.0975 AC: 206 AN: 2112

Alfa AF: 0.0894 Hom.: 1378

Bravo AF: 0.109

Asia WGS AF: 0.0690 AC: 242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.19
DANN	Benign	0.79
PhyloP100		-2.5

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: rs16834831;

hg19: chr1-192759186;