4-5798767-G-A

Position:

chr4-5798767-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_153717.3(EVC):c.2279G>A(p.Arg760Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0172 in 1,611,026 control chromosomes in the GnomAD database, including 479 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R760W) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.016 ( 32 hom., cov: 33)

Exomes 𝑓: 0.017 ( 447 hom. )

Consequence

EVC
NM_153717.3 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: 0.929

Variant links:

Genes affected

EVC (HGNC:3497): (EvC ciliary complex subunit 1) This gene encodes a protein containing a leucine zipper and a transmembrane domain. This gene has been implicated in both Ellis-van Creveld syndrome (EvC) and Weyers acrodental dysostosis. [provided by RefSeq, Jul 2008]

EVC links:

CRMP1 (HGNC:2365): (collapsin response mediator protein 1) This gene encodes a member of a family of cytosolic phosphoproteins expressed exclusively in the nervous system. The encoded protein is thought to be a part of the semaphorin signal transduction pathway implicated in semaphorin-induced growth cone collapse during neural development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2008]

CRMP1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0017463267).

BP6

Variant 4-5798767-G-A is Benign according to our data. Variant chr4-5798767-G-A is described in ClinVar as [Benign]. Clinvar id is 262771.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr4-5798767-G-A is described in Lovd as [Benign]. Variant chr4-5798767-G-A is described in Lovd as [Likely_benign].

BA1

GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EVC	NM_153717.3 linkuse as main transcript	c.2279G>A	p.Arg760Gln	missense_variant	15/21	ENST00000264956.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
EVC	ENST00000264956.11 linkuse as main transcript	c.2279G>A	p.Arg760Gln	missense_variant	15/21	1	NM_153717.3	P1
EVC	ENST00000515113.1 linkuse as main transcript	n.503G>A		non_coding_transcript_exon_variant	3/4	5
CRMP1	ENST00000506216.5 linkuse as main transcript	n.1647+26727C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.0159

AC:

2417

AN:

152178

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00364

Gnomad AMI

AF:

0.0593

Gnomad AMR

AF:

0.0296

Gnomad ASJ

AF:

0.00923

Gnomad EAS

AF:

0.0471

Gnomad SAS

AF:

0.0446

Gnomad FIN

AF:

0.0297

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.0133

Gnomad OTH

AF:

0.0206

GnomAD3 exomes

AF:

0.0248

AC:

6068

AN:

244388

Hom.:

120

AF XY:

0.0251

AC XY:

3349

AN XY:

133454

show subpopulations

Gnomad AFR exome

AF:

0.00339

Gnomad AMR exome

AF:

0.0392

Gnomad ASJ exome

AF:

0.00937

Gnomad EAS exome

AF:

0.0469

Gnomad SAS exome

AF:

0.0468

Gnomad FIN exome

AF:

0.0313

Gnomad NFE exome

AF:

0.0139

Gnomad OTH exome

AF:

0.0205

GnomAD4 exome

AF:

0.0173

AC:

25215

AN:

1458730

Hom.:

447

Cov.:

AF XY:

0.0181

AC XY:

13164

AN XY:

725654

show subpopulations

Gnomad4 AFR exome

AF:

0.00218

Gnomad4 AMR exome

AF:

0.0374

Gnomad4 ASJ exome

AF:

0.00846

Gnomad4 EAS exome

AF:

0.0713

Gnomad4 SAS exome

AF:

0.0456

Gnomad4 FIN exome

AF:

0.0302

Gnomad4 NFE exome

AF:

0.0124

Gnomad4 OTH exome

AF:

0.0177

GnomAD4 genome

AF:

0.0159

AC:

2416

AN:

152296

Hom.:

Cov.:

AF XY:

0.0179

AC XY:

1334

AN XY:

74468

show subpopulations

Gnomad4 AFR

AF:

0.00363

Gnomad4 AMR

AF:

0.0295

Gnomad4 ASJ

AF:

0.00923

Gnomad4 EAS

AF:

0.0472

Gnomad4 SAS

AF:

0.0447

Gnomad4 FIN

AF:

0.0297

Gnomad4 NFE

AF:

0.0133

Gnomad4 OTH

AF:

0.0203

Alfa

AF:

0.0136

Hom.:

Bravo

AF:

0.0149

TwinsUK

AF:

0.0138

AC:

ALSPAC

AF:

0.0122

AC:

ESP6500AA

AF:

0.00252

AC:

ESP6500EA

AF:

0.0142

AC:

121

ExAC

AF:

0.0237

AC:

2870

Asia WGS

AF:

0.0380

AC:

130

AN:

3478

EpiCase

AF:

0.0133

EpiControl

AF:

0.0136

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:4

Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	May 19, 2016	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 04, 2016	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -

Ellis-van Creveld syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 12, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Ellis-van Creveld syndrome;C0457013:Curry-Hall syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Feb 01, 2024

- -

not provided

Benign:1

Likely benign, no assertion criteria provided

clinical testing

Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.083

BayesDel_addAF

Benign

-0.67

BayesDel_noAF

Benign

-0.64

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.12

Eigen

Benign

0.13

Eigen_PC

Benign

0.13

FATHMM_MKL

Benign

0.39

LIST_S2

Benign

0.75

MetaRNN

Benign

0.0017

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.9

MutationTaster

Benign

1.0

N;N

PrimateAI

Benign

0.28

PROVEAN

Benign

-0.95

REVEL

Benign

0.14

Sift

Benign

0.21

Sift4G

Benign

0.10

Polyphen

0.93

Vest4

0.037

ClinPred

0.013

GERP RS

4.2

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Varity_R

0.046

gMVP

0.13

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