Variant chr4-5748087-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_153717.3(EVC):c.940-61C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 1,578,494 control chromosomes in the GnomAD database, including 17,709 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.15 ( 1946 hom., cov: 34)

Exomes 𝑓: 0.13 ( 15763 hom. )

Consequence

EVC
NM_153717.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.440

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 (BayesDel_noAF=-0.8).

BP6

Variant 4-5748087-C-T is Benign according to our data. Variant chr4-5748087-C-T is described in ClinVar as [Benign]. Clinvar id is 1266411.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.415 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.940-61C>T		intron_variant		ENST00000264956.11

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris
EVC	ENST00000264956.11 linkuse as main transcript	c.940-61C>T	intron_variant		1	NM_153717.3	P1
EVC	ENST00000509451.1 linkuse as main transcript	c.940-61C>T	intron_variant		1
CRMP1	ENST00000506216.5 linkuse as main transcript	n.1873G>A	non_coding_transcript_exon_variant	13/13	5

Frequencies

GnomAD3 genomes

AF:

0.147

AC:

22306

AN:

151960

Hom.:

1946

Cov.:

show subpopulations

Gnomad AFR

AF:

0.153

Gnomad AMI

AF:

0.184

Gnomad AMR

AF:

0.200

Gnomad ASJ

AF:

0.177

Gnomad EAS

AF:

0.429

Gnomad SAS

AF:

0.230

Gnomad FIN

AF:

0.100

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.108

Gnomad OTH

AF:

0.161

GnomAD4 exome

AF:

0.130

AC:

185404

AN:

1426416

Hom.:

15763

Cov.:

AF XY:

0.133

AC XY:

94581

AN XY:

712020

show subpopulations

Gnomad4 AFR exome

AF:

0.153

Gnomad4 AMR exome

AF:

0.237

Gnomad4 ASJ exome

AF:

0.176

Gnomad4 EAS exome

AF:

0.440

Gnomad4 SAS exome

AF:

0.224

Gnomad4 FIN exome

AF:

0.0949

Gnomad4 NFE exome

AF:

0.106

Gnomad4 OTH exome

AF:

0.147

GnomAD4 genome

AF:

0.147

AC:

22320

AN:

152078

Hom.:

1946

Cov.:

AF XY:

0.151

AC XY:

11236

AN XY:

74340

show subpopulations

Gnomad4 AFR

AF:

0.153

Gnomad4 AMR

AF:

0.200

Gnomad4 ASJ

AF:

0.177

Gnomad4 EAS

AF:

0.430

Gnomad4 SAS

AF:

0.230

Gnomad4 FIN

AF:

0.100

Gnomad4 NFE

AF:

0.108

Gnomad4 OTH

AF:

0.163

Alfa

AF:

0.118

Hom.:

1196

Bravo

AF:

0.158

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	GeneDx	Jun 25, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

3.8

DANN

Benign

0.75

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