Genetic Variant RARRES2:c.*39G>C (chr7-150338411-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_002889.4(RARRES2):c.*39G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 1,512,648 control chromosomes in the GnomAD database, including 53,725 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 0.25 ( 5183 hom., cov: 33)

Exomes 𝑓: 0.26 ( 48542 hom. )

Consequence

RARRES2
NM_002889.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.50

Publications

17 publications found

Variant links:

Genes affected

RARRES2 (HGNC:9868): (retinoic acid receptor responder 2) This gene encodes a secreted chemotactic protein that initiates chemotaxis via the ChemR23 G protein-coupled seven-transmembrane domain ligand. Expression of this gene is upregulated by the synthetic retinoid tazarotene and occurs in a wide variety of tissues. The active protein has several roles, including that as an adipokine and as an antimicrobial protein with activity against bacteria and fungi. [provided by RefSeq, Nov 2014]

RARRES2 links:

ENSG00000301866 (HGNC:):

ENSG00000301866 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 (MetaRNN=4.4593215E-4).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RARRES2	NM_002889.4 link	c.*39G>C		3_prime_UTR_variant	Exon 6 of 6	ENST00000223271.8	NP_002880.1
RARRES2	XR_007060121.1 link	n.619G>C		non_coding_transcript_exon_variant	Exon 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RARRES2	ENST00000223271.8 link	c.*39G>C		3_prime_UTR_variant	Exon 6 of 6	1	NM_002889.4	ENSP00000223271.3

Frequencies

GnomAD3 genomes

AF:

0.255

AC:

38747

AN:

151976

Hom.:

5189

Cov.:

show subpopulations

Gnomad AFR

AF:

0.235

Gnomad AMI

AF:

0.393

Gnomad AMR

AF:

0.164

Gnomad ASJ

AF:

0.316

Gnomad EAS

AF:

0.283

Gnomad SAS

AF:

0.286

Gnomad FIN

AF:

0.344

Gnomad MID

AF:

0.263

Gnomad NFE

AF:

0.265

Gnomad OTH

AF:

0.233

GnomAD2 exomes

AF:

0.248

AC:

34053

AN:

137218

AF XY:

0.254

show subpopulations

Gnomad AFR exome

AF:

0.227

Gnomad AMR exome

AF:

0.123

Gnomad ASJ exome

AF:

0.332

Gnomad EAS exome

AF:

0.283

Gnomad FIN exome

AF:

0.340

Gnomad NFE exome

AF:

0.265

Gnomad OTH exome

AF:

0.238

GnomAD4 exome

AF:

0.264

AC:

359839

AN:

1360554

Hom.:

48542

Cov.:

AF XY:

0.266

AC XY:

178222

AN XY:

671152

show subpopulations

African (AFR)

AF:

0.236

AC:

7324

AN:

31084

American (AMR)

AF:

0.126

AC:

4390

AN:

34924

Ashkenazi Jewish (ASJ)

AF:

0.329

AC:

8042

AN:

24462

East Asian (EAS)

AF:

0.342

AC:

11528

AN:

33716

South Asian (SAS)

AF:

0.280

AC:

21915

AN:

78172

European-Finnish (FIN)

AF:

0.344

AC:

10894

AN:

31654

Middle Eastern (MID)

AF:

0.254

AC:

1416

AN:

5576

European-Non Finnish (NFE)

AF:

0.263

AC:

279588

AN:

1064488

Other (OTH)

AF:

0.261

AC:

14742

AN:

56478

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.466

Heterozygous variant carriers

13765

27530

41296

55061

68826

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9610

19220

28830

38440

48050

<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:

0.255

AC:

38764

AN:

152094

Hom.:

5183

Cov.:

AF XY:

0.259

AC XY:

19263

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.235

AC:

9765

AN:

41496

American (AMR)

AF:

0.163

AC:

2495

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.316

AC:

1096

AN:

3470

East Asian (EAS)

AF:

0.283

AC:

1463

AN:

5170

South Asian (SAS)

AF:

0.285

AC:

1373

AN:

4818

European-Finnish (FIN)

AF:

0.344

AC:

3640

AN:

10580

Middle Eastern (MID)

AF:

0.252

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.265

AC:

18014

AN:

67964

Other (OTH)

AF:

0.230

AC:

486

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1481

2962

4442

5923

7404

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

412

824

1236

1648

2060

<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:

0.205

Hom.:

704

Bravo

AF:

0.238

TwinsUK

AF:

0.256

AC:

948

ALSPAC

AF:

0.257

AC:

991

ExAC

AF:

0.245

AC:

5891

Asia WGS

AF:

0.275

AC:

960

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.63

BayesDel_noAF

Benign

-0.54

CADD

Benign

0.16

(source)

DANN

Benign

0.59

DEOGEN2

Benign

0.036

Eigen

Benign

-1.3

Eigen_PC

Benign

-1.6

FATHMM_MKL

Benign

0.029

LIST_S2

Benign

0.23

MetaRNN

Benign

0.00045

MetaSVM

Benign

-0.99

PhyloP100

-1.5

PROVEAN

Benign

-1.3

REVEL

Benign

0.019

Sift

Uncertain

0.022

ClinPred

0.0046

GERP RS

-5.0

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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