1-92513798-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001350197.2(EVI5):c.2339G>A(p.Gly780Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,613,076 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 Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. G780G) has been classified as Benign.
Frequency
Consequence
NM_001350197.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EVI5 | NM_001350197.2 | c.2339G>A | p.Gly780Asp | missense_variant | Exon 20 of 20 | ENST00000684568.2 | NP_001337126.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EVI5 | ENST00000684568.2 | c.2339G>A | p.Gly780Asp | missense_variant | Exon 20 of 20 | NM_001350197.2 | ENSP00000506999.1 |
Frequencies
GnomAD3 genomes AF: 0.00000661 AC: 1AN: 151348Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461728Hom.: 0 Cov.: 33 AF XY: 0.0000110 AC XY: 8AN XY: 727160
GnomAD4 genome AF: 0.00000661 AC: 1AN: 151348Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 73856
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2291G>A (p.G764D) alteration is located in exon 18 (coding exon 18) of the EVI5 gene. This alteration results from a G to A substitution at nucleotide position 2291, causing the glycine (G) at amino acid position 764 to be replaced by an aspartic acid (D). 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