rs6428106

Variant names:

• chr1-192585301-G-T
• rs6428106
• ENST00000434300.3:n.164+8298C>A

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+8298C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 151,914 control chromosomes in the GnomAD database, including 1,605 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 0.14 (1605 hom., cov: 31)
• Consequence: RGS2-AS1 ENST00000642855.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.201
• Publications: 2 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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.215 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+8298C>A		intron	N/A
	RGS2-AS1	ENST00000642855.1		n.339+8298C>A		intron	N/A
	RGS2-AS1	ENST00000644058.2		n.564+8298C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21261 AN: 151796 Hom.: 1603 Cov.: 31

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.0772

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.140 AC: 21275 AN: 151914 Hom.: 1605 Cov.: 31 AF XY: 0.144 AC XY: 10696 AN XY: 74254

African (AFR) AF: 0.190 AC: 7860 AN: 41388

American (AMR) AF: 0.107 AC: 1625 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 456 AN: 3468

East Asian (EAS) AF: 0.0777 AC: 402 AN: 5172

South Asian (SAS) AF: 0.227 AC: 1091 AN: 4816

European-Finnish (FIN) AF: 0.173 AC: 1823 AN: 10558

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7703 AN: 67944

Other (OTH) AF: 0.113 AC: 237 AN: 2106

Alfa AF: 0.133 Hom.: 175

Bravo AF: 0.133

Asia WGS AF: 0.160 AC: 556 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.27
PhyloP100		0.20

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6428106; hg19: chr1-192554431;