rs886037764
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000344408.10(EVC2):c.3141G>T(p.Trp1047Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,840 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000344408.10 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EVC2 | NM_147127.5 | c.3141G>T | p.Trp1047Cys | missense_variant | 18/22 | ENST00000344408.10 | NP_667338.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EVC2 | ENST00000344408.10 | c.3141G>T | p.Trp1047Cys | missense_variant | 18/22 | 1 | NM_147127.5 | ENSP00000342144 | P2 | |
EVC2 | ENST00000310917.6 | c.2901G>T | p.Trp967Cys | missense_variant | 18/22 | 1 | ENSP00000311683 | A2 | ||
EVC2 | ENST00000475313.5 | c.2901G>T | p.Trp967Cys | missense_variant, NMD_transcript_variant | 18/23 | 1 | ENSP00000431981 | |||
EVC2 | ENST00000509670.1 | c.*1534G>T | 3_prime_UTR_variant, NMD_transcript_variant | 19/23 | 1 | ENSP00000423876 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251072Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135752
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461840Hom.: 0 Cov.: 35 AF XY: 0.00000138 AC XY: 1AN XY: 727222
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Ellis-van Creveld syndrome;C0457013:Curry-Hall syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 28, 2022 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals affected with EVC2-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.007%). This sequence change replaces tryptophan, which is neutral and slightly polar, with cysteine, which is neutral and slightly polar, at codon 1047 of the EVC2 protein (p.Trp1047Cys). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at