1-107906755-C-T

Variant names:

• chr1-107906755-C-T
• rs10494084
• NM_006113.5:c.205-31738G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006113.5(VAV3):​c.205-31738G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 151,812 control chromosomes in the GnomAD database, including 10,862 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 0.36 (10862 hom., cov: 32)
• Consequence: VAV3 NM_006113.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.774
• Publications: 0 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VAV3	NM_006113.5	c.205-31738G>A		intron_variant	Intron 1 of 26	ENST00000370056.9	NP_006104.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VAV3	ENST00000370056.9	c.205-31738G>A		intron_variant	Intron 1 of 26	1	NM_006113.5	ENSP00000359073.4

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54941 AN: 151694 Hom.: 10824 Cov.: 32

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.305

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.363 AC: 55036 AN: 151812 Hom.: 10862 Cov.: 32 AF XY: 0.363 AC XY: 26924 AN XY: 74188

African (AFR) AF: 0.542 AC: 22426 AN: 41376

American (AMR) AF: 0.251 AC: 3823 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1076 AN: 3468

East Asian (EAS) AF: 0.315 AC: 1630 AN: 5168

South Asian (SAS) AF: 0.421 AC: 2027 AN: 4814

European-Finnish (FIN) AF: 0.304 AC: 3193 AN: 10512

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.293 AC: 19913 AN: 67910

Other (OTH) AF: 0.307 AC: 646 AN: 2106

Alfa AF: 0.347 Hom.: 1277

Bravo AF: 0.361

Asia WGS AF: 0.391 AC: 1361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.54
PhyloP100		-0.77
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10494084; hg19: chr1-108449377;