rs2156323
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001134398.2(VAV2):c.380+5675C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.093 in 152,256 control chromosomes in the GnomAD database, including 817 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.093 ( 817 hom., cov: 33)
Consequence
VAV2
NM_001134398.2 intron
NM_001134398.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -4.67
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 Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VAV2 | NM_001134398.2 | c.380+5675C>T | intron_variant | ENST00000371850.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VAV2 | ENST00000371850.8 | c.380+5675C>T | intron_variant | 1 | NM_001134398.2 | A1 | |||
VAV2 | ENST00000406606.7 | c.380+5675C>T | intron_variant | 1 | P4 | ||||
VAV2 | ENST00000371851.1 | c.380+5675C>T | intron_variant | 5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0932 AC: 14178AN: 152138Hom.: 817 Cov.: 33
GnomAD3 genomes
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0930 AC: 14157AN: 152256Hom.: 817 Cov.: 33 AF XY: 0.0931 AC XY: 6929AN XY: 74442
GnomAD4 genome
?
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14157
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33
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6929
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74442
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398
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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