Variant 7-150338411-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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:

ENSG00000261305 (HGNC:):

ENSG00000261305 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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	Q99969A0A090N7U9
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 link	c.*39G>C		3_prime_UTR_variant	Exon 6 of 6	1	NM_002889.4	ENSP00000223271.3		Q99969

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

GnomAD3 exomes

AF:

0.248

AC:

34053

AN:

137218

Hom.:

4633

AF XY:

0.254

AC XY:

18870

AN XY:

74426

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 SAS exome

AF:

0.281

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

Gnomad4 AFR exome

AF:

0.236

Gnomad4 AMR exome

AF:

0.126

Gnomad4 ASJ exome

AF:

0.329

Gnomad4 EAS exome

AF:

0.342

Gnomad4 SAS exome

AF:

0.280

Gnomad4 FIN exome

AF:

0.344

Gnomad4 NFE exome

AF:

0.263

Gnomad4 OTH exome

AF:

0.261

GnomAD4 genome

AF:

0.255

AC:

38764

AN:

152094

Hom.:

5183

Cov.:

AF XY:

0.259

AC XY:

19263

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.235

Gnomad4 AMR

AF:

0.163

Gnomad4 ASJ

AF:

0.316

Gnomad4 EAS

AF:

0.283

Gnomad4 SAS

AF:

0.285

Gnomad4 FIN

AF:

0.344

Gnomad4 NFE

AF:

0.265

Gnomad4 OTH

AF:

0.230

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

BayesDel_addAF

Benign

-0.63

BayesDel_noAF

Benign

-0.54

CADD

Benign

0.16

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

PROVEAN

Benign

-1.3

REVEL

Benign

0.019

Sift

Uncertain

0.022

ClinPred

0.0046

GERP RS

-5.0

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over