chr2-75518107-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001135032.2(EVA1A):c.34G>A(p.Val12Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000681 in 1,614,144 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 (★).
Frequency
Consequence
NM_001135032.2 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EVA1A | NM_001135032.2 | c.34G>A | p.Val12Met | missense_variant | 3/4 | ENST00000393913.8 | |
EVA1A | NM_001369524.1 | c.34G>A | p.Val12Met | missense_variant | 5/6 | ||
EVA1A | NM_001369525.1 | c.34G>A | p.Val12Met | missense_variant | 4/5 | ||
EVA1A | NM_032181.3 | c.34G>A | p.Val12Met | missense_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EVA1A | ENST00000393913.8 | c.34G>A | p.Val12Met | missense_variant | 3/4 | 1 | NM_001135032.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000171 AC: 43AN: 251046Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 135658
GnomAD4 exome AF: 0.0000677 AC: 99AN: 1461862Hom.: 0 Cov.: 31 AF XY: 0.0000564 AC XY: 41AN XY: 727234
GnomAD4 genome ? AF: 0.0000722 AC: 11AN: 152282Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74466
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 07, 2022 | The c.34G>A (p.V12M) alteration is located in exon 3 (coding exon 1) of the EVA1A gene. This alteration results from a G to A substitution at nucleotide position 34, causing the valine (V) at amino acid position 12 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