19-7860675-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001159944.3(EVI5L):c.1489C>T(p.Leu497Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000126 in 1,587,906 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001159944.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EVI5L | NM_001159944.3 | c.1489C>T | p.Leu497Phe | missense_variant | Exon 14 of 20 | ENST00000538904.7 | NP_001153416.1 | |
EVI5L | NM_145245.5 | c.1456C>T | p.Leu486Phe | missense_variant | Exon 13 of 19 | NP_660288.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EVI5L | ENST00000538904.7 | c.1489C>T | p.Leu497Phe | missense_variant | Exon 14 of 20 | 1 | NM_001159944.3 | ENSP00000445905.1 | ||
EVI5L | ENST00000270530.8 | c.1456C>T | p.Leu486Phe | missense_variant | Exon 13 of 19 | 1 | ENSP00000270530.3 | |||
EVI5L | ENST00000601766.1 | c.91C>T | p.Leu31Phe | missense_variant | Exon 1 of 4 | 3 | ENSP00000470145.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152194Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000487 AC: 1AN: 205482Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 110572
GnomAD4 exome AF: 6.97e-7 AC: 1AN: 1435594Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 711568
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152312Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74484
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1489C>T (p.L497F) alteration is located in exon 13 (coding exon 13) of the EVI5L gene. This alteration results from a C to T substitution at nucleotide position 1489, causing the leucine (L) at amino acid position 497 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at