1-192796813-A-G

Variant names:

• chr1-192796813-A-G
• rs7531013
• ENST00000454090.1:n.211+70A>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.202-30619T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 152,098 control chromosomes in the GnomAD database, including 24,089 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 0.56 (24081 hom., cov: 32)
  • Exomes 𝑓: 0.71 (8 hom.)
• Consequence: RGS2-AS1 ENST00000644058.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.623
• Publications: 2 publications found

Genes affected

ENSG00000228687 (HGNC:):

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.618 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
	ENSG00000228687	ENST00000454090.1	TSL:6	n.211+70A>G		intron	N/A
	RGS2-AS1	ENST00000644058.2		n.202-30619T>C		intron	N/A
	RGS2-AS1	ENST00000644134.1		n.105-30619T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85106 AN: 151946 Hom.: 24049 Cov.: 32

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.556

GnomAD4 exome AF: 0.706 AC: 24 AN: 34 Hom.: 8 Cov.: 0 AF XY: 0.792 AC XY: 19 AN XY: 24

African (AFR) AF: 0.500 AC: 2 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.750 AC: 18 AN: 24

Other (OTH) AF: 0.750 AC: 3 AN: 4

GnomAD4 genome AF: 0.560 AC: 85186 AN: 152064 Hom.: 24081 Cov.: 32 AF XY: 0.556 AC XY: 41372 AN XY: 74350

African (AFR) AF: 0.625 AC: 25892 AN: 41448

American (AMR) AF: 0.528 AC: 8070 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2159 AN: 3472

East Asian (EAS) AF: 0.632 AC: 3275 AN: 5180

South Asian (SAS) AF: 0.608 AC: 2936 AN: 4828

European-Finnish (FIN) AF: 0.425 AC: 4499 AN: 10580

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.535 AC: 36379 AN: 67960

Other (OTH) AF: 0.558 AC: 1180 AN: 2116

Alfa AF: 0.548 Hom.: 89258

Bravo AF: 0.566

Asia WGS AF: 0.652 AC: 2263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	9.8
DANN	Benign	0.52
PhyloP100		0.62

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: rs7531013;

hg19: chr1-192765943;