rs16834456

Variant names:

• chr1-192581407-C-A
• rs16834456
• ENST00000434300.3:n.164+12192G>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.339+12192G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,030 control chromosomes in the GnomAD database, including 2,847 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 (2847 hom., cov: 32)
• Consequence: RGS2-AS1 ENST00000642855.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0510
• Publications: 7 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=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 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.164+12192G>T		intron	N/A
	RGS2-AS1	ENST00000642855.1		n.339+12192G>T		intron	N/A
	RGS2-AS1	ENST00000644058.2		n.564+12192G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22957 AN: 151912 Hom.: 2842 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.0864

Gnomad ASJ AF: 0.0479

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0760

Gnomad FIN AF: 0.0802

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0844

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.151 AC: 22987 AN: 152030 Hom.: 2847 Cov.: 32 AF XY: 0.147 AC XY: 10948 AN XY: 74304

African (AFR) AF: 0.344 AC: 14238 AN: 41420

American (AMR) AF: 0.0861 AC: 1314 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0479 AC: 166 AN: 3466

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5180

South Asian (SAS) AF: 0.0758 AC: 366 AN: 4826

European-Finnish (FIN) AF: 0.0802 AC: 850 AN: 10600

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0844 AC: 5735 AN: 67974

Other (OTH) AF: 0.111 AC: 233 AN: 2104

Alfa AF: 0.127 Hom.: 267

Bravo AF: 0.161

Asia WGS AF: 0.0520 AC: 180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	11
DANN	Benign	0.75
PhyloP100		0.051

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: rs16834456;

hg19: chr1-192550537;