rs12311304

Variant names:

• chr12-15236703-T-C
• rs12311304
• ENST00000393736.3:c.-114-19100A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000393736.3(RERG):​c.-114-19100A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 152,064 control chromosomes in the GnomAD database, including 9,663 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 0.35 (9663 hom., cov: 32)
• Consequence: RERG ENST00000393736.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295
• Publications: 6 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.458 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.-114-19100A>G		intron_variant	Intron 2 of 3	3		ENSP00000440887.1

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52809 AN: 151946 Hom.: 9642 Cov.: 32

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.348 AC: 52869 AN: 152064 Hom.: 9663 Cov.: 32 AF XY: 0.346 AC XY: 25682 AN XY: 74330

African (AFR) AF: 0.464 AC: 19225 AN: 41448

American (AMR) AF: 0.253 AC: 3873 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1178 AN: 3468

East Asian (EAS) AF: 0.239 AC: 1237 AN: 5180

South Asian (SAS) AF: 0.268 AC: 1291 AN: 4824

European-Finnish (FIN) AF: 0.282 AC: 2980 AN: 10576

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.326 AC: 22129 AN: 67974

Other (OTH) AF: 0.325 AC: 685 AN: 2110

Alfa AF: 0.332 Hom.: 4482

Bravo AF: 0.349

Asia WGS AF: 0.283 AC: 984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
DANN	Benign	0.57
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs12311304; hg19: chr12-15389637;