chr2-75493246-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001135032.2(EVA1A):c.449G>A(p.Arg150His) variant causes a missense change. The variant allele was found at a frequency of 0.0469 in 1,611,076 control chromosomes in the GnomAD database, including 2,039 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Genomes: 𝑓 0.052 ( 245 hom., cov: 33)
Exomes 𝑓: 0.046 ( 1794 hom. )
Consequence
EVA1A
NM_001135032.2 missense
NM_001135032.2 missense
Scores
4
2
11
Clinical Significance
Conservation
PhyloP100: 6.07
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 Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0016549826).
BP6
?
Variant 2-75493246-C-T is Benign according to our data. Variant chr2-75493246-C-T is described in ClinVar as [Benign]. Clinvar id is 3056113.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.066 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EVA1A | NM_001135032.2 | c.449G>A | p.Arg150His | missense_variant | 4/4 | ENST00000393913.8 | |
EVA1A | NM_001369524.1 | c.449G>A | p.Arg150His | missense_variant | 6/6 | ||
EVA1A | NM_001369525.1 | c.449G>A | p.Arg150His | missense_variant | 5/5 | ||
EVA1A | NM_032181.3 | c.449G>A | p.Arg150His | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EVA1A | ENST00000393913.8 | c.449G>A | p.Arg150His | missense_variant | 4/4 | 1 | NM_001135032.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0516 AC: 7860AN: 152182Hom.: 245 Cov.: 33
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0412 AC: 10143AN: 246392Hom.: 267 AF XY: 0.0425 AC XY: 5678AN XY: 133526
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GnomAD4 exome AF: 0.0464 AC: 67723AN: 1458776Hom.: 1794 Cov.: 30 AF XY: 0.0464 AC XY: 33636AN XY: 725410
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GnomAD4 genome ? AF: 0.0517 AC: 7867AN: 152300Hom.: 245 Cov.: 33 AF XY: 0.0491 AC XY: 3660AN XY: 74470
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ESP6500AA
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5310
Asia WGS
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
EVA1A-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 13, 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:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Pathogenic
DEOGEN2
Benign
T;T;T;T;T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
MetaRNN
Benign
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
Benign
N;N;N;N;N
REVEL
Benign
Sift
Benign
T;T;T;T;T
Sift4G
Benign
T;T;T;T;T
Polyphen
D;D;D;.;D
Vest4
MPC
1.3
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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Score
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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