chr4-5756299-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_153717.3(EVC):c.1500G>A(p.Met500Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000311 in 1,613,142 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict 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
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EVC | NM_153717.3 | c.1500G>A | p.Met500Ile | missense_variant | 11/21 | ENST00000264956.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EVC | ENST00000264956.11 | c.1500G>A | p.Met500Ile | missense_variant | 11/21 | 1 | NM_153717.3 | P1 | |
EVC | ENST00000509451.1 | c.1500G>A | p.Met500Ile | missense_variant | 11/12 | 1 | |||
CRMP1 | ENST00000506216.5 | n.1648-7987C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00149 AC: 226AN: 152148Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000390 AC: 97AN: 248410Hom.: 0 AF XY: 0.000343 AC XY: 46AN XY: 134200
GnomAD4 exome AF: 0.000189 AC: 276AN: 1460876Hom.: 0 Cov.: 32 AF XY: 0.000173 AC XY: 126AN XY: 726548
GnomAD4 genome AF: 0.00148 AC: 226AN: 152266Hom.: 0 Cov.: 32 AF XY: 0.00159 AC XY: 118AN XY: 74440
ClinVar
Submissions by phenotype
Ellis-van Creveld syndrome Pathogenic:2Uncertain:1Benign:1
Likely pathogenic, no assertion criteria provided | research | University of Washington Center for Mendelian Genomics, University of Washington | - | - - |
Pathogenic, no assertion criteria provided | research | Dan Cohn Lab, University Of California Los Angeles | Jun 01, 2017 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Apr 02, 2018 | - - |
Likely benign, no assertion criteria provided | clinical testing | Natera, Inc. | Feb 17, 2020 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jan 11, 2023 | In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 29068549) - |
Ellis-van Creveld syndrome;C0457013:Curry-Hall syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
EVC-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 28, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at