Genetic Variant ENST00000434300.3:n.106-7215A>G (chr1-192600872-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000434300.3(RGS2-AS1):n.106-7215A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 151,994 control chromosomes in the GnomAD database, including 11,864 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 0.39 ( 11864 hom., cov: 32)

Consequence

RGS2-AS1
ENST00000434300.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.861

Publications

4 publications found

Variant links:

Genes affected

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

RGS2-AS1 links:

LOC105371664 (HGNC:):

LOC105371664 links:

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new If you want to explore the variant's impact on the transcript ENST00000434300.3, 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=-0.98).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000434300.3. 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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
RGS2-AS1	ENST00000434300.3	TSL:5	n.106-7215A>G	intron	N/A
RGS2-AS1	ENST00000642855.1		n.281-7215A>G	intron	N/A
RGS2-AS1	ENST00000644058.2		n.506-7215A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.387

AC:

58816

AN:

151878

Hom.:

11855

Cov.:

show subpopulations

Gnomad AFR

AF:

0.307

Gnomad AMI

AF:

0.360

Gnomad AMR

AF:

0.324

Gnomad ASJ

AF:

0.475

Gnomad EAS

AF:

0.524

Gnomad SAS

AF:

0.543

Gnomad FIN

AF:

0.476

Gnomad MID

AF:

0.411

Gnomad NFE

AF:

0.411

Gnomad OTH

AF:

0.395

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

GnomAD4 genome

AF:

0.387

AC:

58847

AN:

151994

Hom.:

11864

Cov.:

AF XY:

0.394

AC XY:

29278

AN XY:

74286

show subpopulations

African (AFR)

AF:

0.307

AC:

12727

AN:

41480

American (AMR)

AF:

0.323

AC:

4931

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.475

AC:

1644

AN:

3464

East Asian (EAS)

AF:

0.525

AC:

2711

AN:

5168

South Asian (SAS)

AF:

0.541

AC:

2609

AN:

4822

European-Finnish (FIN)

AF:

0.476

AC:

5036

AN:

10578

Middle Eastern (MID)

AF:

0.401

AC:

118

AN:

294

European-Non Finnish (NFE)

AF:

0.411

AC:

27901

AN:

67908

Other (OTH)

AF:

0.400

AC:

842

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1783

3566

5349

7132

8915

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

580

1160

1740

2320

2900

<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:

0.398

Hom.:

1551

Bravo

AF:

0.368

Asia WGS

AF:

0.535

AC:

1861

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

1.4

(source)

DANN

Benign

0.68

PhyloP100

-0.86

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