4-5745350-C-T

Variant summary

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

The NM_153717.3(EVC):​c.939+9C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0009 in 1,612,264 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0021 ( 2 hom., cov: 32)
Exomes 𝑓: 0.00078 ( 10 hom. )

Consequence

EVC
NM_153717.3 intron

Scores

2

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -0.994
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]

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 (BayesDel_noAF=-0.91).
BP6
Variant 4-5745350-C-T is Benign according to our data. Variant chr4-5745350-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 435101.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr4-5745350-C-T is described in Lovd as [Likely_benign].
BS2
High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
EVCNM_153717.3 linkuse as main transcriptc.939+9C>T intron_variant ENST00000264956.11 NP_714928.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
EVCENST00000264956.11 linkuse as main transcriptc.939+9C>T intron_variant 1 NM_153717.3 ENSP00000264956 P1
EVCENST00000509451.1 linkuse as main transcriptc.939+9C>T intron_variant 1 ENSP00000426774

Frequencies

GnomAD3 genomes
AF:
0.00208
AC:
313
AN:
150548
Hom.:
2
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00645
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000526
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000196
Gnomad SAS
AF:
0.00844
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000148
Gnomad OTH
AF:
0.000967
GnomAD3 exomes
AF:
0.00164
AC:
412
AN:
251392
Hom.:
5
AF XY:
0.00196
AC XY:
266
AN XY:
135866
show subpopulations
Gnomad AFR exome
AF:
0.00597
Gnomad AMR exome
AF:
0.000260
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00983
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000880
Gnomad OTH exome
AF:
0.000652
GnomAD4 exome
AF:
0.000779
AC:
1138
AN:
1461594
Hom.:
10
Cov.:
40
AF XY:
0.00103
AC XY:
746
AN XY:
727110
show subpopulations
Gnomad4 AFR exome
AF:
0.00592
Gnomad4 AMR exome
AF:
0.000291
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0101
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000630
Gnomad4 OTH exome
AF:
0.000729
GnomAD4 genome
AF:
0.00208
AC:
313
AN:
150670
Hom.:
2
Cov.:
32
AF XY:
0.00216
AC XY:
159
AN XY:
73570
show subpopulations
Gnomad4 AFR
AF:
0.00643
Gnomad4 AMR
AF:
0.000525
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000196
Gnomad4 SAS
AF:
0.00844
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000148
Gnomad4 OTH
AF:
0.000957
Alfa
AF:
0.00102
Hom.:
1
Bravo
AF:
0.00194
Asia WGS
AF:
0.00462
AC:
16
AN:
3478

ClinVar

Significance: Benign/Likely benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenAug 01, 2022EVC: BS1, BS2 -
Benign, criteria provided, single submitterclinical testingARUP Laboratories, Molecular Genetics and Genomics, ARUP LaboratoriesAug 24, 2020- -
not specified Benign:1
Likely benign, criteria provided, single submitterclinical testingGenetic Services Laboratory, University of ChicagoOct 29, 2015- -
Ellis-van Creveld syndrome Benign:1
Benign, no assertion criteria providedclinical testingNatera, Inc.Sep 16, 2020- -
Ellis-van Creveld syndrome;C0457013:Curry-Hall syndrome Benign:1
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 11, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.024
DANN
Benign
0.74

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.

Other links and lift over

dbSNP: rs201282320; hg19: chr4-5747077; COSMIC: COSV99381480; COSMIC: COSV99381480; API