Genetic Variant RGS17:c.*3201C>T (chr6-153008373-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_012419.5(RGS17):c.*3201C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 150,900 control chromosomes in the GnomAD database, including 5,957 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 0.28 ( 5957 hom., cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

RGS17
NM_012419.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0330

Publications

8 publications found

Variant links:

Genes affected

RGS17 (HGNC:14088): (regulator of G protein signaling 17) This gene encodes a member of the regulator of G-protein signaling family. This protein contains a conserved, 120 amino acid motif called the RGS domain and a cysteine-rich region. The protein attenuates the signaling activity of G-proteins by binding to activated, GTP-bound G alpha subunits and acting as a GTPase activating protein (GAP), increasing the rate of conversion of the GTP to GDP. This hydrolysis allows the G alpha subunits to bind G beta/gamma subunit heterodimers, forming inactive G-protein heterotrimers, thereby terminating the signal. [provided by RefSeq, Jul 2008]

RGS17 links:

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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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
RGS17	NM_012419.5 link	c.*3201C>T	3_prime_UTR_variant	Exon 5 of 5	ENST00000206262.2	NP_036551.3	Q9UGC6
RGS17	XM_047418634.1 link	c.*3201C>T	3_prime_UTR_variant	Exon 5 of 5		XP_047274590.1
RGS17	XM_047418635.1 link	c.*3201C>T	3_prime_UTR_variant	Exon 5 of 5		XP_047274591.1
RGS17	XM_047418636.1 link	c.*3201C>T	3_prime_UTR_variant	Exon 5 of 5		XP_047274592.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RGS17	ENST00000206262.2 link	c.*3201C>T		3_prime_UTR_variant	Exon 5 of 5	1	NM_012419.5	ENSP00000206262.1		Q9UGC6
RGS17	ENST00000367225.6 link	c.*3201C>T		3_prime_UTR_variant	Exon 4 of 4	1		ENSP00000356194.1		Q9UGC6

Frequencies

GnomAD3 genomes

AF:

0.279

AC:

42061

AN:

150822

Hom.:

5950

Cov.:

show subpopulations

Gnomad AFR

AF:

0.271

Gnomad AMI

AF:

0.475

Gnomad AMR

AF:

0.276

Gnomad ASJ

AF:

0.308

Gnomad EAS

AF:

0.330

Gnomad SAS

AF:

0.250

Gnomad FIN

AF:

0.314

Gnomad MID

AF:

0.313

Gnomad NFE

AF:

0.274

Gnomad OTH

AF:

0.259

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.279

AC:

42091

AN:

150900

Hom.:

5957

Cov.:

AF XY:

0.279

AC XY:

20566

AN XY:

73588

show subpopulations

African (AFR)

AF:

0.271

AC:

11133

AN:

41130

American (AMR)

AF:

0.276

AC:

4190

AN:

15180

Ashkenazi Jewish (ASJ)

AF:

0.308

AC:

1069

AN:

3468

East Asian (EAS)

AF:

0.331

AC:

1701

AN:

5144

South Asian (SAS)

AF:

0.250

AC:

1196

AN:

4788

European-Finnish (FIN)

AF:

0.314

AC:

3183

AN:

10136

Middle Eastern (MID)

AF:

0.324

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.274

AC:

18544

AN:

67756

Other (OTH)

AF:

0.261

AC:

548

AN:

2096

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1561

3121

4682

6242

7803

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

430

860

1290

1720

2150

<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:

0.271

Hom.:

3105

Bravo

AF:

0.276

Asia WGS

AF:

0.303

AC:

1054

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.60

(source)

DANN

Benign

0.32

PhyloP100

-0.033

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over