2-75493415-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001135032.2(EVA1A):c.280G>A(p.Asp94Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0000551 in 1,614,200 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00018 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000042 ( 0 hom. )
Consequence
EVA1A
NM_001135032.2 missense
NM_001135032.2 missense
Scores
8
10
Clinical Significance
Conservation
PhyloP100: 6.16
Genes affected
EVA1A (HGNC:25816): (eva-1 homolog A, regulator of programmed cell death) Predicted to be involved in apoptotic process and autophagy. Located in intracellular membrane-bounded organelle and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.16022462).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EVA1A | NM_001135032.2 | c.280G>A | p.Asp94Asn | missense_variant | 4/4 | ENST00000393913.8 | |
EVA1A | NM_001369524.1 | c.280G>A | p.Asp94Asn | missense_variant | 6/6 | ||
EVA1A | NM_001369525.1 | c.280G>A | p.Asp94Asn | missense_variant | 5/5 | ||
EVA1A | NM_032181.3 | c.280G>A | p.Asp94Asn | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EVA1A | ENST00000393913.8 | c.280G>A | p.Asp94Asn | missense_variant | 4/4 | 1 | NM_001135032.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000177 AC: 27AN: 152202Hom.: 0 Cov.: 33
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?
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GnomAD3 exomes AF: 0.000195 AC: 49AN: 251218Hom.: 0 AF XY: 0.000155 AC XY: 21AN XY: 135820
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GnomAD4 exome AF: 0.0000424 AC: 62AN: 1461880Hom.: 0 Cov.: 30 AF XY: 0.0000399 AC XY: 29AN XY: 727244
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GnomAD4 genome ? AF: 0.000177 AC: 27AN: 152320Hom.: 0 Cov.: 33 AF XY: 0.000269 AC XY: 20AN XY: 74480
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 06, 2021 | The c.280G>A (p.D94N) alteration is located in exon 4 (coding exon 2) of the EVA1A gene. This alteration results from a G to A substitution at nucleotide position 280, causing the aspartic acid (D) at amino acid position 94 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T;T;T;T;T;T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
M_CAP
Benign
D
MetaRNN
Benign
T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;M;.;M;.;.
MutationTaster
Benign
D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;D;D;D;D;D
REVEL
Benign
Sift
Benign
D;D;D;D;D;D;D
Sift4G
Uncertain
D;D;D;D;D;.;D
Polyphen
D;D;D;.;D;.;.
Vest4
MVP
MPC
1.2
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at