chr7-150339575-T-G

Position:

• chr7-150339575-T-G

Variant summary

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

The ENST00000223271.8(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 ENST00000223271.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.515

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=-0.86).
• 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/exons	MANE	Protein	UniProt
RARRES2	NM_002889.4	c.280-494A>C		intron_variant		ENST00000223271.8	NP_002880.1
RARRES2	XR_007060121.1	n.352-494A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RARRES2	ENST00000223271.8	c.280-494A>C		intron_variant		1	NM_002889.4	ENSP00000223271	P1
	ENST00000647589.1	n.117+1976T>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.0600

Gnomad4 ASJ AF: 0.0470

Gnomad4 EAS AF: 0.0607

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.0693

Gnomad4 NFE AF: 0.0621

Gnomad4 OTH AF: 0.0975

Alfa AF: 0.0662 Hom.: 472

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

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: rs17173608; hg19: chr7-150036664;