rs17173608

Variant names:

• chr7-150339575-T-G
• rs17173608
• NM_002889.4:c.280-494A>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.280-494A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,186 control chromosomes in the GnomAD database, including 1,397 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 0.11 (1397 hom., cov: 32)
• Consequence: RARRES2 NM_002889.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.515
• Publications: 45 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 (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RARRES2	NM_002889.4	c.280-494A>C		intron_variant	Intron 3 of 5	ENST00000223271.8	NP_002880.1
RARRES2	XR_007060121.1	n.352-494A>C		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RARRES2	ENST00000223271.8	c.280-494A>C		intron_variant	Intron 3 of 5	1	NM_002889.4	ENSP00000223271.3

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16933 AN: 152066 Hom.: 1392 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.0648

Gnomad AMR AF: 0.0602

Gnomad ASJ AF: 0.0470

Gnomad EAS AF: 0.0603

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0693

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0621

Gnomad OTH AF: 0.0943

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.112 AC: 16975 AN: 152186 Hom.: 1397 Cov.: 32 AF XY: 0.112 AC XY: 8308 AN XY: 74402

African (AFR) AF: 0.233 AC: 9652 AN: 41478

American (AMR) AF: 0.0600 AC: 917 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0470 AC: 163 AN: 3470

East Asian (EAS) AF: 0.0607 AC: 314 AN: 5176

South Asian (SAS) AF: 0.141 AC: 679 AN: 4818

European-Finnish (FIN) AF: 0.0693 AC: 735 AN: 10610

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0621 AC: 4226 AN: 68024

Other (OTH) AF: 0.0975 AC: 206 AN: 2112

Alfa AF: 0.0675 Hom.: 1127

Bravo AF: 0.114

Asia WGS AF: 0.107 AC: 373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.55
DANN	Benign	0.64
PhyloP100		-0.52
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: rs17173608; hg19: chr7-150036664;