4-5708462-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_147127.5(EVC2):c.52C>T(p.Leu18Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 1,505,760 control chromosomes in the GnomAD database, including 15,591 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. L18L) has been classified as Likely benign.
Frequency
Consequence
NM_147127.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EVC2 | NM_147127.5 | c.52C>T | p.Leu18Phe | missense_variant | 1/22 | ENST00000344408.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EVC2 | ENST00000344408.10 | c.52C>T | p.Leu18Phe | missense_variant | 1/22 | 1 | NM_147127.5 | P2 | |
EVC2 | ENST00000310917.6 | c.-13+367C>T | intron_variant | 1 | A2 | ||||
EVC2 | ENST00000475313.5 | c.-13+367C>T | intron_variant, NMD_transcript_variant | 1 | |||||
EVC2 | ENST00000509670.1 | c.-106-322C>T | intron_variant, NMD_transcript_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.178 AC: 26979AN: 151866Hom.: 2982 Cov.: 32
GnomAD3 exomes AF: 0.152 AC: 15220AN: 100284Hom.: 1345 AF XY: 0.149 AC XY: 8348AN XY: 56038
GnomAD4 exome AF: 0.128 AC: 173268AN: 1353784Hom.: 12597 Cov.: 31 AF XY: 0.129 AC XY: 85908AN XY: 667562
GnomAD4 genome AF: 0.178 AC: 27045AN: 151976Hom.: 2994 Cov.: 32 AF XY: 0.179 AC XY: 13287AN XY: 74282
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Dec 14, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 08, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Ellis-van Creveld syndrome Benign:2
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Ellis-van Creveld syndrome;C0457013:Curry-Hall syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 29, 2023 | - - |
Curry-Hall syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at