rs12578517

Variant names:

• chr12-15254251-T-C
• rs12578517
• ENST00000393736.3:c.-114-36648A>G

Variant summary

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

The ENST00000393736.3(RERG):​c.-114-36648A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 151,862 control chromosomes in the GnomAD database, including 5,160 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 0.24 (5160 hom., cov: 31)
• Consequence: RERG ENST00000393736.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.684

Genes affected

RERG (HGNC:15980): (RAS like estrogen regulated growth inhibitor) RERG, a member of the RAS superfamily of GTPases, inhibits cell proliferation and tumor formation (Finlin et al., 2001 [PubMed 11533059]).[supplied by OMIM, Mar 2009]

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 (NFE) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RERG	ENST00000393736.3	c.-114-36648A>G		intron_variant	Intron 2 of 3	3		ENSP00000440887.1

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37109 AN: 151744 Hom.: 5160 Cov.: 31

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.244 AC: 37114 AN: 151862 Hom.: 5160 Cov.: 31 AF XY: 0.244 AC XY: 18095 AN XY: 74190

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.243

Alfa AF: 0.286 Hom.: 1612

Bravo AF: 0.232

Asia WGS AF: 0.202 AC: 701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.4
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12578517; hg19: chr12-15407185;