rs17173617

chr7-150340934-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.33

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RARRES2	NM_002889.4	c.-20-305C>G		intron_variant		ENST00000223271.8
RARRES2	XR_007060121.1	n.53-305C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RARRES2	ENST00000223271.8	c.-20-305C>G		intron_variant		1	NM_002889.4	P1
	ENST00000647589.1	n.118-1237G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52284 AN: 151510 Hom.: 10386 Cov.: 31

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.: 0 AF XY: 0.250 AC XY: 10736 AN XY: 42960

Gnomad4 AFR exome AF: 0.530

Gnomad4 AMR exome AF: 0.150

Gnomad4 ASJ exome AF: 0.281

Gnomad4 EAS exome AF: 0.389

Gnomad4 SAS exome AF: 0.237

Gnomad4 FIN exome AF: 0.229

Gnomad4 NFE exome AF: 0.228

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.345 AC: 52366 AN: 151632 Hom.: 10420 Cov.: 31 AF XY: 0.343 AC XY: 25415 AN XY: 74066

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.323

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.308

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.7
Dann	Benign	0.60
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.3

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

Other links and lift over

dbSNP: rs17173617; hg19: chr7-150038023; COSMIC: COSV56231617; COSMIC: COSV56231617;