Variant 17-1937383-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The ENST00000331238.7(RTN4RL1):c.439G>A(p.Gly147Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0117 in 1,613,652 control chromosomes in the GnomAD database, including 120 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.010 ( 10 hom., cov: 32)

Exomes 𝑓: 0.012 ( 110 hom. )

Consequence

RTN4RL1
ENST00000331238.7 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 7.57

Variant links:

Genes affected

RTN4RL1 (HGNC:21329): (reticulon 4 receptor like 1) Enables signaling receptor activity. Predicted to be involved in negative regulation of axon regeneration. Located in cell surface. Is anchored component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

RTN4RL1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.020207763).

BP6

Variant 17-1937383-C-T is Benign according to our data. Variant chr17-1937383-C-T is described in ClinVar as [Benign]. Clinvar id is 774926.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High AC in GnomAd4 at 1571 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RTN4RL1	NM_178568.4 linkuse as main transcript	c.439G>A	p.Gly147Ser	missense_variant	2/2	ENST00000331238.7	NP_848663.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RTN4RL1	ENST00000331238.7 linkuse as main transcript	c.439G>A	p.Gly147Ser	missense_variant	2/2	1	NM_178568.4	ENSP00000330631	P1

Frequencies

GnomAD3 genomes

AF:

0.0103

AC:

1570

AN:

152098

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00749

Gnomad AMI

AF:

0.0362

Gnomad AMR

AF:

0.00911

Gnomad ASJ

AF:

0.00288

Gnomad EAS

AF:

0.00348

Gnomad SAS

AF:

0.00166

Gnomad FIN

AF:

0.00556

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0142

Gnomad OTH

AF:

0.0115

GnomAD3 exomes

AF:

0.00866

AC:

2155

AN:

248744

Hom.:

AF XY:

0.00851

AC XY:

1149

AN XY:

135056

show subpopulations

Gnomad AFR exome

AF:

0.00757

Gnomad AMR exome

AF:

0.00846

Gnomad ASJ exome

AF:

0.00408

Gnomad EAS exome

AF:

0.00428

Gnomad SAS exome

AF:

0.00239

Gnomad FIN exome

AF:

0.00498

Gnomad NFE exome

AF:

0.0124

Gnomad OTH exome

AF:

0.00894

GnomAD4 exome

AF:

0.0118

AC:

17235

AN:

1461436

Hom.:

110

Cov.:

AF XY:

0.0115

AC XY:

8330

AN XY:

727020

show subpopulations

Gnomad4 AFR exome

AF:

0.00777

Gnomad4 AMR exome

AF:

0.00908

Gnomad4 ASJ exome

AF:

0.00409

Gnomad4 EAS exome

AF:

0.00418

Gnomad4 SAS exome

AF:

0.00191

Gnomad4 FIN exome

AF:

0.00435

Gnomad4 NFE exome

AF:

0.0137

Gnomad4 OTH exome

AF:

0.0109

GnomAD4 genome

AF:

0.0103

AC:

1571

AN:

152216

Hom.:

Cov.:

AF XY:

0.00962

AC XY:

716

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.00749

Gnomad4 AMR

AF:

0.00909

Gnomad4 ASJ

AF:

0.00288

Gnomad4 EAS

AF:

0.00348

Gnomad4 SAS

AF:

0.00186

Gnomad4 FIN

AF:

0.00556

Gnomad4 NFE

AF:

0.0142

Gnomad4 OTH

AF:

0.0114

Alfa

AF:

0.0124

Hom.:

Bravo

AF:

0.0105

TwinsUK

AF:

0.0127

AC:

ALSPAC

AF:

0.0140

AC:

ESP6500AA

AF:

0.00693

AC:

ESP6500EA

AF:

0.0132

AC:

113

ExAC

AF:

0.00847

AC:

1026

Asia WGS

AF:

0.00462

AC:

AN:

3478

EpiCase

AF:

0.0117

EpiControl

AF:

0.0114

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 05, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.21

BayesDel_addAF

Benign

-0.38

BayesDel_noAF

Benign

-0.31

CADD

Pathogenic

DANN

Uncertain

1.0

DEOGEN2

Uncertain

0.42

Eigen

Pathogenic

0.78

Eigen_PC

Pathogenic

0.78

FATHMM_MKL

Pathogenic

1.0

LIST_S2

Uncertain

0.90

MetaRNN

Benign

0.020

MetaSVM

Benign

-0.55

MutationAssessor

Benign

0.75

MutationTaster

Benign

1.0

PrimateAI

Uncertain

0.62

PROVEAN

Pathogenic

-5.2

REVEL

Uncertain

0.37

Sift

Uncertain

0.0050

Sift4G

Uncertain

0.045

Polyphen

1.0

Vest4

0.73

MVP

0.39

MPC

1.2

ClinPred

0.025

GERP RS

5.7

Varity_R

0.48

gMVP

0.63

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over