chr2-75493462-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_001135032.2(EVA1A):c.233G>A(p.Ser78Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00044 in 1,614,254 control chromosomes in the GnomAD database, including 4 homozygotes. 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 Benign (★).
Frequency
Consequence
NM_001135032.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EVA1A | NM_001135032.2 | c.233G>A | p.Ser78Asn | missense_variant | 4/4 | ENST00000393913.8 | |
EVA1A | NM_001369524.1 | c.233G>A | p.Ser78Asn | missense_variant | 6/6 | ||
EVA1A | NM_001369525.1 | c.233G>A | p.Ser78Asn | missense_variant | 5/5 | ||
EVA1A | NM_032181.3 | c.233G>A | p.Ser78Asn | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EVA1A | ENST00000393913.8 | c.233G>A | p.Ser78Asn | missense_variant | 4/4 | 1 | NM_001135032.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000611 AC: 93AN: 152268Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000896 AC: 225AN: 251246Hom.: 1 AF XY: 0.000810 AC XY: 110AN XY: 135820
GnomAD4 exome AF: 0.000422 AC: 617AN: 1461868Hom.: 4 Cov.: 31 AF XY: 0.000411 AC XY: 299AN XY: 727234
GnomAD4 genome ? AF: 0.000610 AC: 93AN: 152386Hom.: 0 Cov.: 33 AF XY: 0.000792 AC XY: 59AN XY: 74530
ClinVar
Submissions by phenotype
EVA1A-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 28, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at