4-5622978-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_147127.5(EVC2):c.2060G>T(p.Arg687Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,613,498 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign 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. R687C) has been classified as Uncertain significance.
Frequency
Consequence
NM_147127.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EVC2 | NM_147127.5 | c.2060G>T | p.Arg687Leu | missense_variant | 14/22 | ENST00000344408.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EVC2 | ENST00000344408.10 | c.2060G>T | p.Arg687Leu | missense_variant | 14/22 | 1 | NM_147127.5 | P2 | |
EVC2 | ENST00000310917.6 | c.1820G>T | p.Arg607Leu | missense_variant | 14/22 | 1 | A2 | ||
EVC2 | ENST00000475313.5 | c.1820G>T | p.Arg607Leu | missense_variant, NMD_transcript_variant | 14/23 | 1 | |||
EVC2 | ENST00000509670.1 | c.*453G>T | 3_prime_UTR_variant, NMD_transcript_variant | 15/23 | 1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152160Hom.: 0 Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461338Hom.: 0 Cov.: 35 AF XY: 0.00 AC XY: 0AN XY: 727002
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152160Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74334
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at