chr4-5748087-C-CGTTTG
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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
NM_153717.3 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -2.00
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]
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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 |
---|---|---|---|---|---|---|---|
EVC | NM_153717.3 | c.940-59_940-55dup | intron_variant | ENST00000264956.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EVC | ENST00000264956.11 | c.940-59_940-55dup | intron_variant | 1 | NM_153717.3 | P1 | |||
EVC | ENST00000509451.1 | c.940-59_940-55dup | intron_variant | 1 | |||||
CRMP1 | ENST00000506216.5 | n.1872_1873insCAAAC | non_coding_transcript_exon_variant | 13/13 | 5 |
Frequencies
GnomAD3 genomes AF: 0.104 AC: 15754AN: 151944Hom.: 1150 Cov.: 32
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GnomAD4 exome AF: 0.0684 AC: 97645AN: 1426530Hom.: 4068 Cov.: 28 AF XY: 0.0674 AC XY: 48001AN XY: 712074
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GnomAD4 genome AF: 0.104 AC: 15766AN: 152062Hom.: 1150 Cov.: 32 AF XY: 0.102 AC XY: 7563AN XY: 74330
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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 submitter | clinical testing | GeneDx | Jun 17, 2020 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at