12-15144123-T-C

Variant names:

• chr12-15144123-T-C
• rs4763417
• NM_032918.3:c.62-23004A>G

Variant summary

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

The NM_032918.3(RERG):​c.62-23004A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.664 in 151,902 control chromosomes in the GnomAD database, including 33,579 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 0.66 (33579 hom., cov: 30)
• Consequence: RERG NM_032918.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RERG	NM_032918.3	c.62-23004A>G		intron_variant	Intron 2 of 4	ENST00000256953.6	NP_116307.1
RERG	NM_001190726.2	c.62-32706A>G		intron_variant	Intron 2 of 3		NP_001177655.1
RERG	XM_047429797.1	c.-128-415A>G		intron_variant	Intron 1 of 4		XP_047285753.1
RERG	XM_047429798.1	c.62-23004A>G		intron_variant	Intron 2 of 5		XP_047285754.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RERG	ENST00000256953.6	c.62-23004A>G		intron_variant	Intron 2 of 4	1	NM_032918.3	ENSP00000256953.2

Frequencies

GnomAD3 genomes AF: 0.664 AC: 100740 AN: 151786 Hom.: 33559 Cov.: 30

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.672

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.664 AC: 100820 AN: 151902 Hom.: 33579 Cov.: 30 AF XY: 0.664 AC XY: 49250 AN XY: 74224

African (AFR) AF: 0.641 AC: 26528 AN: 41390

American (AMR) AF: 0.747 AC: 11409 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2302 AN: 3472

East Asian (EAS) AF: 0.583 AC: 3005 AN: 5150

South Asian (SAS) AF: 0.598 AC: 2874 AN: 4808

European-Finnish (FIN) AF: 0.663 AC: 7005 AN: 10560

Middle Eastern (MID) AF: 0.620 AC: 181 AN: 292

European-Non Finnish (NFE) AF: 0.672 AC: 45668 AN: 67946

Other (OTH) AF: 0.653 AC: 1375 AN: 2106

Alfa AF: 0.672 Hom.: 109151

Bravo AF: 0.670

Asia WGS AF: 0.637 AC: 2212 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	2.5
DANN	Benign	0.80
PhyloP100		-0.021
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs4763417; hg19: chr12-15297057;