chr12-15254251-T-C

Position:

• chr12-15254251-T-C

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]

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.15254251T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RERG	ENST00000393736.3	c.-114-36648A>G		intron_variant		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;