chr4-5748087-C-CGTTTG

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_153717.3(EVC):​c.940-59_940-55dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0718 in 1,578,592 control chromosomes in the GnomAD database, including 5,218 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.10 ( 1150 hom., cov: 32)
Exomes 𝑓: 0.068 ( 4068 hom. )

Consequence

EVC
NM_153717.3 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.00
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]
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
Variant 4-5748087-C-CGTTTG is Benign according to our data. Variant chr4-5748087-C-CGTTTG is described in ClinVar as [Benign]. Clinvar id is 1231697.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
EVCNM_153717.3 linkuse as main transcriptc.940-59_940-55dup intron_variant ENST00000264956.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
EVCENST00000264956.11 linkuse as main transcriptc.940-59_940-55dup intron_variant 1 NM_153717.3 P1
EVCENST00000509451.1 linkuse as main transcriptc.940-59_940-55dup intron_variant 1
CRMP1ENST00000506216.5 linkuse as main transcriptn.1872_1873insCAAAC non_coding_transcript_exon_variant 13/135

Frequencies

GnomAD3 genomes
AF:
0.104
AC:
15754
AN:
151944
Hom.:
1150
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.210
Gnomad AMI
AF:
0.0769
Gnomad AMR
AF:
0.0654
Gnomad ASJ
AF:
0.0703
Gnomad EAS
AF:
0.000582
Gnomad SAS
AF:
0.0426
Gnomad FIN
AF:
0.0715
Gnomad MID
AF:
0.0981
Gnomad NFE
AF:
0.0668
Gnomad OTH
AF:
0.110
GnomAD4 exome
AF:
0.0684
AC:
97645
AN:
1426530
Hom.:
4068
Cov.:
28
AF XY:
0.0674
AC XY:
48001
AN XY:
712074
show subpopulations
Gnomad4 AFR exome
AF:
0.216
Gnomad4 AMR exome
AF:
0.0452
Gnomad4 ASJ exome
AF:
0.0684
Gnomad4 EAS exome
AF:
0.000329
Gnomad4 SAS exome
AF:
0.0456
Gnomad4 FIN exome
AF:
0.0679
Gnomad4 NFE exome
AF:
0.0689
Gnomad4 OTH exome
AF:
0.0743
GnomAD4 genome
AF:
0.104
AC:
15766
AN:
152062
Hom.:
1150
Cov.:
32
AF XY:
0.102
AC XY:
7563
AN XY:
74330
show subpopulations
Gnomad4 AFR
AF:
0.210
Gnomad4 AMR
AF:
0.0652
Gnomad4 ASJ
AF:
0.0703
Gnomad4 EAS
AF:
0.000583
Gnomad4 SAS
AF:
0.0418
Gnomad4 FIN
AF:
0.0715
Gnomad4 NFE
AF:
0.0668
Gnomad4 OTH
AF:
0.109
Alfa
AF:
0.0935
Hom.:
99

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJun 17, 2020- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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.

Other links and lift over

dbSNP: rs58769270; hg19: chr4-5749814; API