rs3758239

chr9-5306824-A-G

Variant summary

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

The XM_047423709.1(RLN2):c.-1196T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 151,900 control chromosomes in the GnomAD database, including 3,687 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 0.21 (3687 hom., cov: 31)
• Consequence: RLN2 XM_047423709.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.77

Genes affected

RLN2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RLN2	XM_047423709.1	c.-1196T>C		5_prime_UTR_variant	2/3
RLN2	XM_047423707.1	c.-62-1076T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32380 AN: 151780 Hom.: 3680 Cov.: 31

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.213 AC: 32422 AN: 151900 Hom.: 3687 Cov.: 31 AF XY: 0.213 AC XY: 15785 AN XY: 74222

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.210

Alfa AF: 0.190 Hom.: 5775

Bravo AF: 0.214

Asia WGS AF: 0.234 AC: 814 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.9
Dann	Benign	0.56

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3758239; hg19: chr9-5306824;