chr1-192933285-T-C

Variant names:

• chr1-192933285-T-C
• rs842796
• ENST00000646606.1:n.295+14028A>G

Variant summary

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

The ENST00000646606.1(RGS2-AS1):​n.295+14028A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.616 in 151,990 control chromosomes in the GnomAD database, including 29,055 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 0.62 (29055 hom., cov: 32)
• Consequence: RGS2-AS1 ENST00000646606.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.126
• Publications: 5 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=-0.54).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000646606.1. 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	ENST00000646606.1		n.295+14028A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.616 AC: 93538 AN: 151872 Hom.: 29012 Cov.: 32

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.616 AC: 93635 AN: 151990 Hom.: 29055 Cov.: 32 AF XY: 0.614 AC XY: 45567 AN XY: 74256

African (AFR) AF: 0.671 AC: 27808 AN: 41430

American (AMR) AF: 0.592 AC: 9031 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.619 AC: 2150 AN: 3472

East Asian (EAS) AF: 0.450 AC: 2322 AN: 5164

South Asian (SAS) AF: 0.637 AC: 3074 AN: 4826

European-Finnish (FIN) AF: 0.558 AC: 5891 AN: 10550

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.609 AC: 41367 AN: 67970

Other (OTH) AF: 0.586 AC: 1237 AN: 2112

Alfa AF: 0.608 Hom.: 117919

Bravo AF: 0.619

Asia WGS AF: 0.587 AC: 2038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	15
DANN	Benign	0.70
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs842796; hg19: chr1-192902415; COSMIC: COSV71625402;