4-5689175-T-C

Position:

chr4-5689175-T-C

Variant summary

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

The NM_147127.5(EVC2):c.688A>G(p.Ser230Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 1,613,956 control chromosomes in the GnomAD database, including 41,951 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.22 ( 3753 hom., cov: 33)

Exomes 𝑓: 0.23 ( 38198 hom. )

Consequence

EVC2
NM_147127.5 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.22

Variant links:

Genes affected

EVC2 (HGNC:19747): (EvC ciliary complex subunit 2) This gene encodes a protein that functions in bone formation and skeletal development. Mutations in this gene, as well as in a neighboring gene that lies in a head-to-head configuration, cause Ellis-van Creveld syndrome, an autosomal recessive skeletal dysplasia that is also known as chondroectodermal dysplasia. Mutations in this gene also cause acrofacial dysostosis Weyers type, also referred to as Curry-Hall syndrome, a disease that combines limb and facial abnormalities. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]

EVC2 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=0.004810661).

BP6

Variant 4-5689175-T-C is Benign according to our data. Variant chr4-5689175-T-C is described in ClinVar as [Benign]. Clinvar id is 262620.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr4-5689175-T-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EVC2	NM_147127.5 linkuse as main transcript	c.688A>G	p.Ser230Gly	missense_variant	5/22	ENST00000344408.10	NP_667338.3	Q86UK5-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
EVC2	ENST00000344408.10 linkuse as main transcript	c.688A>G	p.Ser230Gly	missense_variant	5/22	1	NM_147127.5	ENSP00000342144.5	Q86UK5-1
EVC2	ENST00000310917.6 linkuse as main transcript	c.448A>G	p.Ser150Gly	missense_variant	5/22	1		ENSP00000311683.2	Q86UK5-2
EVC2	ENST00000475313.5 linkuse as main transcript	n.448A>G		non_coding_transcript_exon_variant	5/23	1		ENSP00000431981.1	A0A0C4DGE7
EVC2	ENST00000509670.1 linkuse as main transcript	n.448A>G		non_coding_transcript_exon_variant	6/23	1		ENSP00000423876.1	E9PFT2

Frequencies

GnomAD3 genomes

AF:

0.221

AC:

33675

AN:

152042

Hom.:

3746

Cov.:

show subpopulations

Gnomad AFR

AF:

0.196

Gnomad AMI

AF:

0.139

Gnomad AMR

AF:

0.238

Gnomad ASJ

AF:

0.231

Gnomad EAS

AF:

0.385

Gnomad SAS

AF:

0.274

Gnomad FIN

AF:

0.229

Gnomad MID

AF:

0.196

Gnomad NFE

AF:

0.217

Gnomad OTH

AF:

0.236

GnomAD3 exomes

AF:

0.239

AC:

60173

AN:

251426

Hom.:

7513

AF XY:

0.241

AC XY:

32755

AN XY:

135876

show subpopulations

Gnomad AFR exome

AF:

0.196

Gnomad AMR exome

AF:

0.252

Gnomad ASJ exome

AF:

0.220

Gnomad EAS exome

AF:

0.398

Gnomad SAS exome

AF:

0.260

Gnomad FIN exome

AF:

0.231

Gnomad NFE exome

AF:

0.214

Gnomad OTH exome

AF:

0.234

GnomAD4 exome

AF:

0.226

AC:

330040

AN:

1461796

Hom.:

38198

Cov.:

AF XY:

0.227

AC XY:

164757

AN XY:

727188

show subpopulations

Gnomad4 AFR exome

AF:

0.188

Gnomad4 AMR exome

AF:

0.250

Gnomad4 ASJ exome

AF:

0.224

Gnomad4 EAS exome

AF:

0.347

Gnomad4 SAS exome

AF:

0.258

Gnomad4 FIN exome

AF:

0.227

Gnomad4 NFE exome

AF:

0.219

Gnomad4 OTH exome

AF:

0.229

GnomAD4 genome

AF:

0.221

AC:

33693

AN:

152160

Hom.:

3753

Cov.:

AF XY:

0.225

AC XY:

16703

AN XY:

74390

show subpopulations

Gnomad4 AFR

AF:

0.196

Gnomad4 AMR

AF:

0.238

Gnomad4 ASJ

AF:

0.231

Gnomad4 EAS

AF:

0.386

Gnomad4 SAS

AF:

0.273

Gnomad4 FIN

AF:

0.229

Gnomad4 NFE

AF:

0.217

Gnomad4 OTH

AF:

0.232

Alfa

AF:

0.222

Hom.:

9748

Bravo

AF:

0.222

TwinsUK

AF:

0.224

AC:

831

ALSPAC

AF:

0.226

AC:

871

ESP6500AA

AF:

0.201

AC:

887

ESP6500EA

AF:

0.216

AC:

1856

ExAC

AF:

0.236

AC:

28714

Asia WGS

AF:

0.302

AC:

1047

AN:

3478

EpiCase

AF:

0.221

EpiControl

AF:

0.222

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 03, 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, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -

Ellis-van Creveld syndrome

Benign:2

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. -
Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 30, 2021	- -

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

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Curry-Hall syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 30, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.086

BayesDel_addAF

Benign

-0.53

BayesDel_noAF

Benign

-0.40

CADD

Benign

DANN

Benign

0.80

DEOGEN2

Benign

0.051

T;.

Eigen

Benign

-0.87

Eigen_PC

Benign

-0.80

FATHMM_MKL

Benign

0.59

LIST_S2

Benign

0.61

T;T

MetaRNN

Benign

0.0048

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.0

N;.

PrimateAI

Benign

0.29

PROVEAN

Benign

-0.94

N;N

REVEL

Benign

0.099

Sift

Benign

0.13

T;T

Sift4G

Uncertain

0.025

D;D

Polyphen

0.081

B;.

Vest4

0.042

MPC

0.020

ClinPred

0.0024

GERP RS

1.9

Varity_R

0.067

gMVP

0.47

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