17-76007381-C-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001988.4(EVPL):c.5824G>T(p.Gly1942Trp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000138 in 1,446,378 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G1942R) has been classified as Uncertain significance.
Frequency
Consequence
NM_001988.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EVPL | ENST00000301607.8 | c.5824G>T | p.Gly1942Trp | missense_variant | Exon 22 of 22 | 1 | NM_001988.4 | ENSP00000301607.3 | ||
EVPL | ENST00000586740.1 | c.5890G>T | p.Gly1964Trp | missense_variant | Exon 22 of 22 | 1 | ENSP00000465630.1 | |||
EVPL | ENST00000589231.1 | c.61G>T | p.Gly21Trp | missense_variant | Exon 1 of 2 | 3 | ENSP00000467717.1 | |||
EVPL | ENST00000587569.5 | n.6293G>T | non_coding_transcript_exon_variant | Exon 20 of 20 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000138 AC: 2AN: 1446378Hom.: 0 Cov.: 30 AF XY: 0.00000140 AC XY: 1AN XY: 716802
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at