Variant rs2269371 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_002910.6(RENBP):c.851A>G(p.Asp284Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0169 in 1,206,212 control chromosomes in the GnomAD database, including 700 homozygotes. There are 6,087 hemizygotes in GnomAD. 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 0.047 ( 252 hom., 1297 hem., cov: 20)

Exomes 𝑓: 0.014 ( 448 hom. 4790 hem. )

Consequence

RENBP
NM_002910.6 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.26

Variant links:

Genes affected

RENBP (HGNC:9959): (renin binding protein) The gene product inhibits renin activity by forming a dimer with renin, a complex known as high molecular weight renin. The encoded protein contains a leucine zipper domain, which is essential for its dimerization with renin. The gene product can catalyze the interconversion of N-acetylglucosamine to N-acetylmannosamine, indicating that it is a GlcNAc 2-epimerase. Transcript variants utilizing alternative promoters have been described in the literature. [provided by RefSeq, Jul 2008]

RENBP links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RENBP	NM_002910.6 linkuse as main transcript	c.851A>G	p.Asp284Gly	missense_variant	8/11	ENST00000393700.8
RENBP	XM_017029698.2 linkuse as main transcript	c.821A>G	p.Asp274Gly	missense_variant	8/11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RENBP	ENST00000393700.8 linkuse as main transcript	c.851A>G	p.Asp284Gly	missense_variant	8/11	1	NM_002910.6	P1

Frequencies

GnomAD3 genomes

AF:

0.0475

AC:

5169

AN:

108796

Hom.:

253

Cov.:

AF XY:

0.0416

AC XY:

1295

AN XY:

31136

show subpopulations

Gnomad AFR

AF:

0.137

Gnomad AMI

AF:

0.0223

Gnomad AMR

AF:

0.0490

Gnomad ASJ

AF:

0.00230

Gnomad EAS

AF:

0.0267

Gnomad SAS

AF:

0.0276

Gnomad FIN

AF:

0.00384

Gnomad MID

AF:

0.00851

Gnomad NFE

AF:

0.00641

Gnomad OTH

AF:

0.0415

GnomAD3 exomes

AF:

0.0318

AC:

5812

AN:

182935

Hom.:

221

AF XY:

0.0255

AC XY:

1723

AN XY:

67663

show subpopulations

Gnomad AFR exome

AF:

0.134

Gnomad AMR exome

AF:

0.0936

Gnomad ASJ exome

AF:

0.00348

Gnomad EAS exome

AF:

0.0202

Gnomad SAS exome

AF:

0.0255

Gnomad FIN exome

AF:

0.00387

Gnomad NFE exome

AF:

0.00637

Gnomad OTH exome

AF:

0.0244

GnomAD4 exome

AF:

0.0139

AC:

15230

AN:

1097368

Hom.:

448

Cov.:

AF XY:

0.0132

AC XY:

4790

AN XY:

362836

show subpopulations

Gnomad4 AFR exome

AF:

0.149

Gnomad4 AMR exome

AF:

0.0862

Gnomad4 ASJ exome

AF:

0.00480

Gnomad4 EAS exome

AF:

0.0325

Gnomad4 SAS exome

AF:

0.0270

Gnomad4 FIN exome

AF:

0.00323

Gnomad4 NFE exome

AF:

0.00547

Gnomad4 OTH exome

AF:

0.0203

GnomAD4 genome

AF:

0.0475

AC:

5167

AN:

108844

Hom.:

252

Cov.:

AF XY:

0.0416

AC XY:

1297

AN XY:

31194

show subpopulations

Gnomad4 AFR

AF:

0.137

Gnomad4 AMR

AF:

0.0486

Gnomad4 ASJ

AF:

0.00230

Gnomad4 EAS

AF:

0.0265

Gnomad4 SAS

AF:

0.0281

Gnomad4 FIN

AF:

0.00384

Gnomad4 NFE

AF:

0.00641

Gnomad4 OTH

AF:

0.0410

Alfa

AF:

0.0324

Hom.:

326

Bravo

AF:

0.0562

ESP6500AA

AF:

0.127

AC:

488

ESP6500EA

AF:

0.00550

AC:

ExAC

AF:

0.0307

AC:

3723

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.61

BayesDel_noAF

Benign

-0.54

Cadd

Benign

Dann

Uncertain

0.99

DEOGEN2

Benign

0.36

T;.

FATHMM_MKL

Benign

0.60

LIST_S2

Benign

0.74

T;T

MetaRNN

Benign

0.0019

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.5

M;.

MutationTaster

Benign

0.071

P;P;P

PrimateAI

Benign

0.32

PROVEAN

Uncertain

-3.1

D;D

REVEL

Benign

0.13

Sift

Uncertain

0.017

D;D

Sift4G

Uncertain

0.028

D;D

Polyphen

0.12

B;.

Vest4

0.17

MPC

0.63

ClinPred

0.034

GERP RS

5.2

Varity_R

0.39

gMVP

0.49

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.26

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.26

Position offset: 1

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over