chr4-5748190-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_153717.3(EVC):c.982C>T(p.Leu328Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000725 in 1,614,228 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_153717.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EVC | ENST00000264956.11 | c.982C>T | p.Leu328Phe | missense_variant | Exon 8 of 21 | 1 | NM_153717.3 | ENSP00000264956.6 | ||
EVC | ENST00000509451.1 | c.982C>T | p.Leu328Phe | missense_variant | Exon 8 of 12 | 1 | ENSP00000426774.1 | |||
CRMP1 | ENST00000506216.5 | n.1770G>A | non_coding_transcript_exon_variant | Exon 13 of 13 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152218Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000227 AC: 57AN: 251488Hom.: 1 AF XY: 0.000206 AC XY: 28AN XY: 135920
GnomAD4 exome AF: 0.0000643 AC: 94AN: 1461892Hom.: 1 Cov.: 47 AF XY: 0.0000701 AC XY: 51AN XY: 727246
GnomAD4 genome AF: 0.000151 AC: 23AN: 152336Hom.: 0 Cov.: 33 AF XY: 0.000201 AC XY: 15AN XY: 74494
ClinVar
Submissions by phenotype
Ellis-van Creveld syndrome Uncertain:1Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
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not provided Uncertain:1
In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Identified in a patient with Jeune asphyxiating thoracic dystrophy in the published literature (McInerney-Leo et al., 2015) who also had a variant in the DNYC2H1 gene and a homozygous variant in the TTC21B gene that was felt to be the cause of the patient's phenotype; This variant is associated with the following publications: (PMID: 28253570, 25492405) -
Ellis-van Creveld syndrome;C0457013:Curry-Hall syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at