Genetic Variant RGS2-AS1:n.859+913C>T (chr1-192475126-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is . The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000642855.1(RGS2-AS1):n.859+913C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0466 in 152,194 control chromosomes in the GnomAD database, including 182 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 0.047 ( 182 hom., cov: 32)

Consequence

RGS2-AS1
ENST00000642855.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.89

Publications

3 publications found

Variant links:

Genes affected

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

RGS2-AS1 links:

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new If you want to explore the variant's impact on the transcript ENST00000642855.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0867 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	ENST00000642855.1		n.859+913C>T		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0466

AC:

7083

AN:

152076

Hom.:

179

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0273

Gnomad AMI

AF:

0.120

Gnomad AMR

AF:

0.0320

Gnomad ASJ

AF:

0.0427

Gnomad EAS

AF:

0.0936

Gnomad SAS

AF:

0.0689

Gnomad FIN

AF:

0.0889

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.0491

Gnomad OTH

AF:

0.0407

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

GnomAD4 genome

AF:

0.0466

AC:

7086

AN:

152194

Hom.:

182

Cov.:

AF XY:

0.0478

AC XY:

3557

AN XY:

74406

show subpopulations

African (AFR)

AF:

0.0275

AC:

1141

AN:

41532

American (AMR)

AF:

0.0319

AC:

488

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.0427

AC:

148

AN:

3470

East Asian (EAS)

AF:

0.0936

AC:

485

AN:

5182

South Asian (SAS)

AF:

0.0685

AC:

330

AN:

4818

European-Finnish (FIN)

AF:

0.0889

AC:

942

AN:

10594

Middle Eastern (MID)

AF:

0.0646

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0491

AC:

3339

AN:

68000

Other (OTH)

AF:

0.0403

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

347

694

1042

1389

1736

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

172

258

344

430

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0479

Hom.:

Bravo

AF:

0.0412

Asia WGS

AF:

0.0810

AC:

280

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

2.1

(source)

DANN

Benign

0.46

PhyloP100

1.9

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.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over