rs113870218
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_153717.3(EVC):c.384+41C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 1,566,498 control chromosomes in the GnomAD database, including 8,668 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.085 ( 611 hom., cov: 32)
Exomes 𝑓: 0.10 ( 8057 hom. )
Consequence
EVC
NM_153717.3 intron
NM_153717.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.70
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
?
Variant 4-5729431-C-T is Benign according to our data. Variant chr4-5729431-C-T is described in ClinVar as [Benign]. Clinvar id is 262780.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EVC | NM_153717.3 | c.384+41C>T | intron_variant | ENST00000264956.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EVC | ENST00000264956.11 | c.384+41C>T | intron_variant | 1 | NM_153717.3 | P1 | |||
EVC | ENST00000509451.1 | c.384+41C>T | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0849 AC: 12900AN: 151912Hom.: 610 Cov.: 32
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GnomAD3 exomes AF: 0.0908 AC: 22800AN: 251230Hom.: 1222 AF XY: 0.0945 AC XY: 12833AN XY: 135780
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GnomAD4 exome AF: 0.103 AC: 145467AN: 1414468Hom.: 8057 Cov.: 24 AF XY: 0.104 AC XY: 73311AN XY: 706702
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GnomAD4 genome ? AF: 0.0848 AC: 12898AN: 152030Hom.: 611 Cov.: 32 AF XY: 0.0826 AC XY: 6139AN XY: 74294
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Ellis-van Creveld syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Pars Genome Lab | Jun 15, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 07, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at