Genetic Variant RARRES2:c.-20-305C>G (chr7-150340934-G-C) – 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.-20-305C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 236,798 control chromosomes in the GnomAD database, including 13,470 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 0.35 ( 10420 hom., cov: 31)

Exomes 𝑓: 0.25 ( 3050 hom. )

Consequence

RARRES2
NM_002889.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.33

Publications

11 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:

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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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002889.4. 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
	RARRES2	NM_002889.4	MANE Select	c.-20-305C>G		intron	N/A	NP_002880.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
RARRES2	ENST00000223271.8	TSL:1 MANE Select	c.-20-305C>G	intron	N/A	ENSP00000223271.3
RARRES2	ENST00000482669.1	TSL:1	c.-20-305C>G	intron	N/A	ENSP00000418483.1
RARRES2	ENST00000478771.2	TSL:2	n.727C>G	non_coding_transcript_exon	Exon 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.345

AC:

52284

AN:

151510

Hom.:

10386

Cov.:

show subpopulations

Gnomad AFR

AF:

0.561

Gnomad AMI

AF:

0.396

Gnomad AMR

AF:

0.207

Gnomad ASJ

AF:

0.316

Gnomad EAS

AF:

0.324

Gnomad SAS

AF:

0.330

Gnomad FIN

AF:

0.254

Gnomad MID

AF:

0.291

Gnomad NFE

AF:

0.264

Gnomad OTH

AF:

0.309

GnomAD4 exome

AF:

0.252

AC:

21471

AN:

85166

Hom.:

3050

Cov.:

AF XY:

0.250

AC XY:

10736

AN XY:

42960

show subpopulations

African (AFR)

AF:

0.530

AC:

1410

AN:

2658

American (AMR)

AF:

0.150

AC:

393

AN:

2624

Ashkenazi Jewish (ASJ)

AF:

0.281

AC:

995

AN:

3538

East Asian (EAS)

AF:

0.389

AC:

2558

AN:

6568

South Asian (SAS)

AF:

0.237

AC:

503

AN:

2118

European-Finnish (FIN)

AF:

0.229

AC:

1224

AN:

5348

Middle Eastern (MID)

AF:

0.291

AC:

138

AN:

474

European-Non Finnish (NFE)

AF:

0.228

AC:

12780

AN:

55950

Other (OTH)

AF:

0.250

AC:

1470

AN:

5888

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

758

1517

2275

3034

3792

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

192

288

384

480

<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:

0.345

AC:

52366

AN:

151632

Hom.:

10420

Cov.:

AF XY:

0.343

AC XY:

25415

AN XY:

74066

show subpopulations

African (AFR)

AF:

0.562

AC:

23222

AN:

41340

American (AMR)

AF:

0.206

AC:

3150

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.316

AC:

1095

AN:

3470

East Asian (EAS)

AF:

0.323

AC:

1652

AN:

5108

South Asian (SAS)

AF:

0.328

AC:

1578

AN:

4806

European-Finnish (FIN)

AF:

0.254

AC:

2669

AN:

10512

Middle Eastern (MID)

AF:

0.276

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.264

AC:

17910

AN:

67826

Other (OTH)

AF:

0.308

AC:

649

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1573

3146

4718

6291

7864

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

500

1000

1500

2000

2500

<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:

0.322

Hom.:

1092

Bravo

AF:

0.350

Asia WGS

AF:

0.344

AC:

1199

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.7

(source)

DANN

Benign

0.60

PhyloP100

-4.3

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.3

Mutation Taster

=300/0

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