Variant rs11189513 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001351015.2(R3HCC1L):c.1697A>G(p.His566Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 1,613,216 control chromosomes in the GnomAD database, including 83,396 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.27 ( 6264 hom., cov: 32)

Exomes 𝑓: 0.32 ( 77132 hom. )

Consequence

R3HCC1L
NM_001351015.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0250

Variant links:

Genes affected

R3HCC1L (HGNC:23512): (R3H domain and coiled-coil containing 1 like) Colocalizes with exon-exon junction complex. [provided by Alliance of Genome Resources, Apr 2022]

R3HCC1L links:

R3HCC1L (HGNC:):

R3HCC1L links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=3.4430623E-4).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
R3HCC1L	NM_001351015.2 linkuse as main transcript	c.1697A>G	p.His566Arg	missense_variant	5/10	ENST00000298999.8	NP_001337944.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
R3HCC1L	ENST00000298999.8 linkuse as main transcript	c.1697A>G	p.His566Arg	missense_variant	5/10	5	NM_001351015.2	ENSP00000298999.3		A0A384DVK4

Frequencies

GnomAD3 genomes

AF:

0.270

AC:

41049

AN:

151908

Hom.:

6267

Cov.:

show subpopulations

Gnomad AFR

AF:

0.121

Gnomad AMI

AF:

0.247

Gnomad AMR

AF:

0.357

Gnomad ASJ

AF:

0.293

Gnomad EAS

AF:

0.311

Gnomad SAS

AF:

0.422

Gnomad FIN

AF:

0.313

Gnomad MID

AF:

0.263

Gnomad NFE

AF:

0.320

Gnomad OTH

AF:

0.274

GnomAD3 exomes

AF:

0.328

AC:

82457

AN:

251024

Hom.:

14310

AF XY:

0.334

AC XY:

45307

AN XY:

135636

show subpopulations

Gnomad AFR exome

AF:

0.119

Gnomad AMR exome

AF:

0.417

Gnomad ASJ exome

AF:

0.290

Gnomad EAS exome

AF:

0.322

Gnomad SAS exome

AF:

0.421

Gnomad FIN exome

AF:

0.305

Gnomad NFE exome

AF:

0.316

Gnomad OTH exome

AF:

0.326

GnomAD4 exome

AF:

0.320

AC:

468214

AN:

1461190

Hom.:

77132

Cov.:

AF XY:

0.324

AC XY:

235170

AN XY:

726902

show subpopulations

Gnomad4 AFR exome

AF:

0.114

Gnomad4 AMR exome

AF:

0.410

Gnomad4 ASJ exome

AF:

0.293

Gnomad4 EAS exome

AF:

0.269

Gnomad4 SAS exome

AF:

0.424

Gnomad4 FIN exome

AF:

0.307

Gnomad4 NFE exome

AF:

0.318

Gnomad4 OTH exome

AF:

0.316

GnomAD4 genome

AF:

0.270

AC:

41054

AN:

152026

Hom.:

6264

Cov.:

AF XY:

0.273

AC XY:

20275

AN XY:

74288

show subpopulations

Gnomad4 AFR

AF:

0.121

Gnomad4 AMR

AF:

0.357

Gnomad4 ASJ

AF:

0.293

Gnomad4 EAS

AF:

0.311

Gnomad4 SAS

AF:

0.423

Gnomad4 FIN

AF:

0.313

Gnomad4 NFE

AF:

0.320

Gnomad4 OTH

AF:

0.271

Alfa

AF:

0.307

Hom.:

18565

Bravo

AF:

0.264

TwinsUK

AF:

0.309

AC:

1145

ALSPAC

AF:

0.322

AC:

1242

ESP6500AA

AF:

0.127

AC:

559

ESP6500EA

AF:

0.301

AC:

2591

ExAC

AF:

0.322

AC:

39104

Asia WGS

AF:

0.350

AC:

1218

AN:

3478

EpiCase

AF:

0.317

EpiControl

AF:

0.310

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.073

BayesDel_addAF

Benign

-0.82

BayesDel_noAF

Benign

-0.80

CADD

Benign

2.0

DANN

Benign

0.64

DEOGEN2

Benign

0.0035

.;.;T;.

Eigen

Benign

-1.0

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.029

LIST_S2

Benign

0.37

.;.;T;T

MetaRNN

Benign

0.00034

T;T;T;T

MetaSVM

Benign

-0.90

MutationAssessor

Benign

1.1

.;.;L;.

PrimateAI

Benign

0.29

PROVEAN

Benign

-1.8

N;N;.;.

REVEL

Benign

0.021

Sift

Benign

0.15

T;T;.;.

Sift4G

Benign

0.55

T;T;T;T

Polyphen

0.010

.;.;B;.

Vest4

0.030

MPC

0.018

ClinPred

0.014

GERP RS

-2.0

Varity_R

0.045

gMVP

0.035

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

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