12-15254251-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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]

ENSG00000305218 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000393736.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RERG	ENST00000393736.3	TSL:3	c.-114-36648A>G		intron	N/A	ENSP00000440887.1
	ENSG00000305218	ENST00000809668.1		n.-74A>G		upstream_gene	N/A

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

African (AFR) AF: 0.123 AC: 5079 AN: 41426

American (AMR) AF: 0.211 AC: 3212 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1179 AN: 3462

East Asian (EAS) AF: 0.124 AC: 639 AN: 5146

South Asian (SAS) AF: 0.249 AC: 1198 AN: 4810

European-Finnish (FIN) AF: 0.282 AC: 2981 AN: 10556

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.325 AC: 22043 AN: 67896

Other (OTH) AF: 0.243 AC: 514 AN: 2112

Alfa AF: 0.282 Hom.: 1618

Bravo AF: 0.232

Asia WGS AF: 0.202 AC: 701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.4
DANN	Benign	0.59
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs12578517; hg19: chr12-15407185;