9-133772008-T-C
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001134398.2(VAV2):āc.2174A>Gā(p.Lys725Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000098 in 102,044 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 (ā ).
Frequency
Genomes: š 0.0000098 ( 0 hom., cov: 31)
Consequence
VAV2
NM_001134398.2 missense
NM_001134398.2 missense
Scores
1
3
13
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 7.49
Genes affected
VAV2 (HGNC:12658): (vav guanine nucleotide exchange factor 2) VAV2 is the second member of the VAV guanine nucleotide exchange factor family of oncogenes. Unlike VAV1, which is expressed exclusively in hematopoietic cells, VAV2 transcripts were found in most tissues. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2008]
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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=0.23112091).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VAV2 | NM_001134398.2 | c.2174A>G | p.Lys725Arg | missense_variant | 26/30 | ENST00000371850.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VAV2 | ENST00000371850.8 | c.2174A>G | p.Lys725Arg | missense_variant | 26/30 | 1 | NM_001134398.2 | A1 | |
VAV2 | ENST00000406606.7 | c.2144A>G | p.Lys715Arg | missense_variant | 24/27 | 1 | P4 | ||
VAV2 | ENST00000371851.1 | c.2144A>G | p.Lys715Arg | missense_variant | 24/28 | 5 | A1 |
Frequencies
GnomAD3 genomes AF: 0.00000980 AC: 1AN: 102044Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.00000805 AC: 2AN: 248380Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134230
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GnomAD4 exome Cov.: 33
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GnomAD4 genome AF: 0.00000980 AC: 1AN: 102044Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 50152
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
B;D;B
Vest4
MutPred
0.45
.;Loss of ubiquitination at K725 (P = 0.0199);.;
MVP
MPC
0.34
ClinPred
T
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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