NM_002889.4:c.*39G>C

Variant names:

• chr7-150338411-C-G
• rs1047575
• NM_002889.4:c.*39G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 17 publications found

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]

ENSG00000301866 (HGNC:):

ACMG classification

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.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RARRES2	NM_002889.4	MANE Select	c.*39G>C		3_prime_UTR	Exon 6 of 6	NP_002880.1	A0A090N7U9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RARRES2	ENST00000223271.8	TSL:1 MANE Select	c.*39G>C		3_prime_UTR	Exon 6 of 6	ENSP00000223271.3	Q99969
	RARRES2	ENST00000467793.5	TSL:3	c.404G>C	p.Arg135Pro	missense	Exon 5 of 5	ENSP00000417669.1	C9J8S2
	RARRES2	ENST00000466675.5	TSL:2	c.*39G>C		3_prime_UTR	Exon 5 of 5	ENSP00000418009.1	Q99969

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38747 AN: 151976 Hom.: 5189 Cov.: 33

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

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.: 33 AF XY: 0.266 AC XY: 178222 AN XY: 671152

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

GnomAD4 genome AF: 0.255 AC: 38764 AN: 152094 Hom.: 5183 Cov.: 33 AF XY: 0.259 AC XY: 19263 AN XY: 74330

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: 74 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 18014 AN: 67964

Other (OTH) AF: 0.230 AC: 486 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Benign	-0.63	T
BayesDel_noAF	Benign	-0.54
CADD	Benign	0.16
DANN	Benign	0.59
DEOGEN2	Benign	0.036	T
Eigen	Benign	-1.3
Eigen_PC	Benign	-1.6
FATHMM_MKL	Benign	0.029	N
LIST_S2	Benign	0.23	T
MetaRNN	Benign	0.00045	T
MetaSVM	Benign	-0.99	T
PhyloP100		-1.5
PROVEAN	Benign	-1.3	N
REVEL	Benign	0.019
Sift	Uncertain	0.022	D
ClinPred		0.0046	T
GERP RS		-5.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1047575; hg19: chr7-150035500; COSMIC: COSV107300281; COSMIC: COSV107300281;