dbSNP rs11545787: RASD1:c.*161C>T (chr17-17494964-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_016084.5(RASD1):c.*161C>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 0.226 in 872,972 control chromosomes in the GnomAD database, including 23,333 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 0.20 ( 3260 hom., cov: 33)

Exomes 𝑓: 0.23 ( 20073 hom. )

Consequence

RASD1
NM_016084.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.21

Publications

19 publications found

Variant links:

Genes affected

RASD1 (HGNC:15828): (ras related dexamethasone induced 1) This gene encodes a member of the Ras superfamily of small GTPases and is induced by dexamethasone. The encoded protein is an activator of G-protein signaling and acts as a direct nucleotide exchange factor for Gi-Go proteins. This protein interacts with the neuronal nitric oxide adaptor protein CAPON, and a nuclear adaptor protein FE65, which interacts with the Alzheimer's disease amyloid precursor protein. This gene may play a role in dexamethasone-induced alterations in cell morphology, growth and cell-extracellular matrix interactions. Epigenetic inactivation of this gene is closely correlated with resistance to dexamethasone in multiple myeloma cells. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Sep 2011]

RASD1 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=-0.57).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RASD1	NM_016084.5 link	c.*161C>T		3_prime_UTR_variant	Exon 2 of 2	ENST00000225688.4	NP_057168.1	Q9Y272-1
RASD1	NM_001199989.2 link	c.*564C>T		3_prime_UTR_variant	Exon 2 of 2		NP_001186918.1	Q9Y272-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RASD1	ENST00000225688.4 link	c.*161C>T		3_prime_UTR_variant	Exon 2 of 2	1	NM_016084.5	ENSP00000225688.3		Q9Y272-1
RASD1	ENST00000579152.1 link	c.*564C>T		3_prime_UTR_variant	Exon 2 of 2	2		ENSP00000463388.1		Q9Y272-2

Frequencies

GnomAD3 genomes

AF:

0.199

AC:

30226

AN:

152044

Hom.:

3260

Cov.:

show subpopulations

Gnomad AFR

AF:

0.144

Gnomad AMI

AF:

0.219

Gnomad AMR

AF:

0.174

Gnomad ASJ

AF:

0.268

Gnomad EAS

AF:

0.0737

Gnomad SAS

AF:

0.256

Gnomad FIN

AF:

0.183

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.241

Gnomad OTH

AF:

0.208

GnomAD4 exome

AF:

0.231

AC:

166735

AN:

720810

Hom.:

20073

Cov.:

AF XY:

0.233

AC XY:

85332

AN XY:

366586

show subpopulations

African (AFR)

AF:

0.143

AC:

2189

AN:

15326

American (AMR)

AF:

0.180

AC:

3297

AN:

18332

Ashkenazi Jewish (ASJ)

AF:

0.266

AC:

3977

AN:

14974

East Asian (EAS)

AF:

0.0802

AC:

2504

AN:

31236

South Asian (SAS)

AF:

0.257

AC:

13328

AN:

51800

European-Finnish (FIN)

AF:

0.192

AC:

6617

AN:

34534

Middle Eastern (MID)

AF:

0.181

AC:

456

AN:

2520

European-Non Finnish (NFE)

AF:

0.245

AC:

126635

AN:

517436

Other (OTH)

AF:

0.223

AC:

7732

AN:

34652

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

6855

13710

20564

27419

34274

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3144

6288

9432

12576

15720

<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:

0.199

AC:

30236

AN:

152162

Hom.:

3260

Cov.:

AF XY:

0.195

AC XY:

14499

AN XY:

74402

show subpopulations

African (AFR)

AF:

0.144

AC:

5993

AN:

41538

American (AMR)

AF:

0.174

AC:

2660

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.268

AC:

929

AN:

3470

East Asian (EAS)

AF:

0.0736

AC:

381

AN:

5174

South Asian (SAS)

AF:

0.257

AC:

1238

AN:

4808

European-Finnish (FIN)

AF:

0.183

AC:

1937

AN:

10594

Middle Eastern (MID)

AF:

0.177

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.241

AC:

16414

AN:

67968

Other (OTH)

AF:

0.205

AC:

432

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1229

2459

3688

4918

6147

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

340

680

1020

1360

1700

<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:

0.222

Hom.:

6501

Bravo

AF:

0.193

Asia WGS

AF:

0.174

AC:

606

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

(source)

DANN

Benign

0.93

PhyloP100

1.2

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over