17-76007414-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001988.4(EVPL):c.5791G>A(p.Val1931Met) variant causes a missense change. The variant allele was found at a frequency of 0.000112 in 1,603,940 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
NM_001988.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EVPL | ENST00000301607.8 | c.5791G>A | p.Val1931Met | missense_variant | Exon 22 of 22 | 1 | NM_001988.4 | ENSP00000301607.3 | ||
EVPL | ENST00000586740.1 | c.5857G>A | p.Val1953Met | missense_variant | Exon 22 of 22 | 1 | ENSP00000465630.1 | |||
EVPL | ENST00000589231.1 | c.28G>A | p.Val10Met | missense_variant | Exon 1 of 2 | 3 | ENSP00000467717.1 | |||
EVPL | ENST00000587569.5 | n.6260G>A | non_coding_transcript_exon_variant | Exon 20 of 20 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000493 AC: 75AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000141 AC: 35AN: 247836Hom.: 0 AF XY: 0.000127 AC XY: 17AN XY: 133936
GnomAD4 exome AF: 0.0000723 AC: 105AN: 1451642Hom.: 0 Cov.: 31 AF XY: 0.0000749 AC XY: 54AN XY: 720540
GnomAD4 genome AF: 0.000492 AC: 75AN: 152298Hom.: 0 Cov.: 32 AF XY: 0.000577 AC XY: 43AN XY: 74466
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.5791G>A (p.V1931M) alteration is located in exon 22 (coding exon 22) of the EVPL gene. This alteration results from a G to A substitution at nucleotide position 5791, causing the valine (V) at amino acid position 1931 to be replaced by a methionine (M). 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