Genetic Variant VAV3:c.*808A>G (chr1-107572523-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006113.5(VAV3):c.*808A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.903 in 152,666 control chromosomes in the GnomAD database, including 62,546 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 0.90 ( 62343 hom., cov: 32)

Exomes 𝑓: 0.96 ( 203 hom. )

Consequence

VAV3
NM_006113.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.61

Publications

5 publications found

Variant links:

Genes affected

VAV3 (HGNC:12659): (vav guanine nucleotide exchange factor 3) This gene is a member of the VAV gene family. The VAV proteins are guanine nucleotide exchange factors (GEFs) for Rho family GTPases that activate pathways leading to actin cytoskeletal rearrangements and transcriptional alterations. This gene product acts as a GEF preferentially for RhoG, RhoA, and to a lesser extent, RAC1, and it associates maximally with the nucleotide-free states of these GTPases. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Jul 2008]

VAV3 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VAV3	NM_006113.5 link	c.*808A>G		3_prime_UTR_variant	Exon 27 of 27	ENST00000370056.9	NP_006104.4	Q9UKW4-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VAV3	ENST00000370056.9 link	c.*808A>G		3_prime_UTR_variant	Exon 27 of 27	1	NM_006113.5	ENSP00000359073.4		Q9UKW4-1
VAV3	ENST00000527011.5 link	c.*808A>G		3_prime_UTR_variant	Exon 28 of 28	1		ENSP00000432540.1		Q9UKW4-4

Frequencies

GnomAD3 genomes

AF:

0.903

AC:

137374

AN:

152112

Hom.:

62312

Cov.:

show subpopulations

Gnomad AFR

AF:

0.807

Gnomad AMI

AF:

0.908

Gnomad AMR

AF:

0.947

Gnomad ASJ

AF:

0.916

Gnomad EAS

AF:

0.999

Gnomad SAS

AF:

0.937

Gnomad FIN

AF:

0.951

Gnomad MID

AF:

0.892

Gnomad NFE

AF:

0.933

Gnomad OTH

AF:

0.914

GnomAD4 exome

AF:

0.963

AC:

420

AN:

436

Hom.:

203

Cov.:

AF XY:

0.966

AC XY:

255

AN XY:

264

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.962

AC:

408

AN:

424

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

1.00

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.539

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.903

AC:

137461

AN:

152230

Hom.:

62343

Cov.:

AF XY:

0.906

AC XY:

67414

AN XY:

74430

show subpopulations

African (AFR)

AF:

0.807

AC:

33478

AN:

41504

American (AMR)

AF:

0.947

AC:

14502

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.916

AC:

3181

AN:

3472

East Asian (EAS)

AF:

0.999

AC:

5178

AN:

5182

South Asian (SAS)

AF:

0.938

AC:

4516

AN:

4816

European-Finnish (FIN)

AF:

0.951

AC:

10084

AN:

10604

Middle Eastern (MID)

AF:

0.891

AC:

262

AN:

294

European-Non Finnish (NFE)

AF:

0.933

AC:

63496

AN:

68024

Other (OTH)

AF:

0.915

AC:

1936

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

654

1308

1962

2616

3270

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.923

Hom.:

81088

Bravo

AF:

0.899

Asia WGS

AF:

0.957

AC:

3329

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.18

(source)

DANN

Benign

0.46

PhyloP100

-1.6

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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1-107572523-T-C

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over