rs11808092
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001350197.2(EVI5):c.1884G>T(p.Gln628His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 1,603,890 control chromosomes in the GnomAD database, including 45,581 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.20 ( 3454 hom., cov: 31)
Exomes 𝑓: 0.23 ( 42127 hom. )
Consequence
EVI5
NM_001350197.2 missense
NM_001350197.2 missense
Scores
6
12
Clinical Significance
Conservation
PhyloP100: 0.721
Genes affected
EVI5 (HGNC:3501): (ecotropic viral integration site 5) Enables GTPase activator activity and small GTPase binding activity. Involved in positive regulation of GTPase activity and retrograde transport, endosome to Golgi. Located in cytosol. [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=0.0014106333).
BP6
?
Variant 1-92607671-C-A is Benign according to our data. Variant chr1-92607671-C-A is described in ClinVar as [Benign]. Clinvar id is 402837.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EVI5 | NM_001350197.2 | c.1884G>T | p.Gln628His | missense_variant | 17/20 | ENST00000684568.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EVI5 | ENST00000684568.2 | c.1884G>T | p.Gln628His | missense_variant | 17/20 | NM_001350197.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.196 AC: 29697AN: 151808Hom.: 3454 Cov.: 31
GnomAD3 genomes
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GnomAD3 exomes AF: 0.195 AC: 47734AN: 244648Hom.: 5390 AF XY: 0.197 AC XY: 25994AN XY: 132264
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GnomAD4 exome AF: 0.233 AC: 337719AN: 1451964Hom.: 42127 Cov.: 28 AF XY: 0.230 AC XY: 166281AN XY: 722290
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GnomAD4 genome ? AF: 0.196 AC: 29711AN: 151926Hom.: 3454 Cov.: 31 AF XY: 0.194 AC XY: 14423AN XY: 74218
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TwinsUK
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969
ALSPAC
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988
ESP6500AA
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467
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2206
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23595
Asia WGS
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.
MutationTaster
Benign
P;P;P
PrimateAI
Benign
T
PROVEAN
Uncertain
D;.
REVEL
Benign
Sift
Benign
D;.
Sift4G
Uncertain
D;D
Polyphen
B;.
Vest4
MutPred
0.18
.;Loss of ubiquitination at K625 (P = 0.091);
MPC
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