chr5-84064787-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_005711.5(EDIL3):c.865A>G(p.Ile289Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000948 in 1,613,936 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 Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I289M) has been classified as Uncertain significance.
Frequency
Consequence
NM_005711.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EDIL3 | NM_005711.5 | c.865A>G | p.Ile289Val | missense_variant | 8/11 | ENST00000296591.10 | |
EDIL3 | NM_001278642.1 | c.835A>G | p.Ile279Val | missense_variant | 7/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EDIL3 | ENST00000296591.10 | c.865A>G | p.Ile289Val | missense_variant | 8/11 | 1 | NM_005711.5 | P1 | |
EDIL3 | ENST00000380138.3 | c.835A>G | p.Ile279Val | missense_variant | 7/10 | 1 | |||
EDIL3 | ENST00000510271.1 | n.414A>G | non_coding_transcript_exon_variant | 3/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000191 AC: 29AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000454 AC: 114AN: 251086Hom.: 0 AF XY: 0.000427 AC XY: 58AN XY: 135718
GnomAD4 exome AF: 0.0000848 AC: 124AN: 1461630Hom.: 1 Cov.: 31 AF XY: 0.0000701 AC XY: 51AN XY: 727120
GnomAD4 genome ? AF: 0.000190 AC: 29AN: 152306Hom.: 0 Cov.: 32 AF XY: 0.000201 AC XY: 15AN XY: 74488
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 17, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at