Genetic Variant NM_002928.4:c.387+98G>A (chr1-182601868-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_002928.4(RGS16):c.387+98G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 1,477,400 control chromosomes in the GnomAD database, including 276,972 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 0.55 ( 24366 hom., cov: 32)

Exomes 𝑓: 0.61 ( 252606 hom. )

Consequence

RGS16
NM_002928.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.743

Publications

11 publications found

Variant links:

Genes affected

RGS16 (HGNC:9997): (regulator of G protein signaling 16) The protein encoded by this gene belongs to the 'regulator of G protein signaling' family. It inhibits signal transduction by increasing the GTPase activity of G protein alpha subunits. It also may play a role in regulating the kinetics of signaling in the phototransduction cascade. [provided by RefSeq, Jul 2008]

RGS16 links:

Genome browser will be placed here

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=-0.8).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002928.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RGS16	NM_002928.4	MANE Select	c.387+98G>A		intron	N/A	NP_002919.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
RGS16	ENST00000367558.6	TSL:1 MANE Select	c.387+98G>A	intron	N/A	ENSP00000356529.5
RGS16	ENST00000898513.1		c.384+98G>A	intron	N/A	ENSP00000568572.1
RGS16	ENST00000921546.1		c.381+98G>A	intron	N/A	ENSP00000591605.1

Frequencies

GnomAD3 genomes

AF:

0.552

AC:

83834

AN:

151992

Hom.:

24351

Cov.:

show subpopulations

Gnomad AFR

AF:

0.361

Gnomad AMI

AF:

0.594

Gnomad AMR

AF:

0.674

Gnomad ASJ

AF:

0.695

Gnomad EAS

AF:

0.714

Gnomad SAS

AF:

0.676

Gnomad FIN

AF:

0.620

Gnomad MID

AF:

0.665

Gnomad NFE

AF:

0.598

Gnomad OTH

AF:

0.588

GnomAD2 exomes

AF:

0.637

AC:

154779

AN:

242938

AF XY:

0.637

show subpopulations

Gnomad AFR exome

AF:

0.353

Gnomad AMR exome

AF:

0.795

Gnomad ASJ exome

AF:

0.686

Gnomad EAS exome

AF:

0.727

Gnomad FIN exome

AF:

0.618

Gnomad NFE exome

AF:

0.601

Gnomad OTH exome

AF:

0.633

GnomAD4 exome

AF:

0.614

AC:

813269

AN:

1325290

Hom.:

252606

Cov.:

AF XY:

0.616

AC XY:

409944

AN XY:

665398

show subpopulations

African (AFR)

AF:

0.349

AC:

10700

AN:

30690

American (AMR)

AF:

0.786

AC:

34694

AN:

44162

Ashkenazi Jewish (ASJ)

AF:

0.684

AC:

17036

AN:

24890

East Asian (EAS)

AF:

0.710

AC:

27620

AN:

38900

South Asian (SAS)

AF:

0.679

AC:

55968

AN:

82412

European-Finnish (FIN)

AF:

0.620

AC:

32635

AN:

52660

Middle Eastern (MID)

AF:

0.669

AC:

2758

AN:

4124

European-Non Finnish (NFE)

AF:

0.602

AC:

597569

AN:

991858

Other (OTH)

AF:

0.617

AC:

34289

AN:

55594

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

14906

29812

44717

59623

74529

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

15670

31340

47010

62680

78350

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.551

AC:

83885

AN:

152110

Hom.:

24366

Cov.:

AF XY:

0.557

AC XY:

41414

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.361

AC:

14985

AN:

41492

American (AMR)

AF:

0.675

AC:

10314

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.695

AC:

2411

AN:

3468

East Asian (EAS)

AF:

0.714

AC:

3681

AN:

5156

South Asian (SAS)

AF:

0.678

AC:

3273

AN:

4830

European-Finnish (FIN)

AF:

0.620

AC:

6570

AN:

10592

Middle Eastern (MID)

AF:

0.677

AC:

199

AN:

294

European-Non Finnish (NFE)

AF:

0.598

AC:

40671

AN:

67966

Other (OTH)

AF:

0.587

AC:

1239

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1855

3711

5566

7422

9277

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

724

1448

2172

2896

3620

<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:

0.581

Hom.:

4805

Bravo

AF:

0.548

Asia WGS

AF:

0.648

AC:

2249

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

3.9

(source)

DANN

Benign

0.65

PhyloP100

-0.74

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over