Variant chr9-133772055-A-ACACACGGCCCCGGCGGTCACTGCGTGAGGGC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001134398.2(VAV2):c.2136-10_2136-9insGCCCTCACGCAGTGACCGCCGGGGCCGTGTG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 1,448,216 control chromosomes in the GnomAD database, including 115,689 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.35 ( 9887 hom., cov: 37)

Exomes 𝑓: 0.39 ( 115689 hom. )

Failed GnomAD Quality Control

Consequence

VAV2
NM_001134398.2 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.47

Variant links:

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]

VAV2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 9-133772055-A-ACACACGGCCCCGGCGGTCACTGCGTGAGGGC is Benign according to our data. Variant chr9-133772055-A-ACACACGGCCCCGGCGGTCACTGCGTGAGGGC is described in ClinVar as [Benign]. Clinvar id is 768335.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAdExome4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VAV2	NM_001134398.2 link	c.2136-10_2136-9insGCCCTCACGCAGTGACCGCCGGGGCCGTGTG		intron_variant		ENST00000371850.8	NP_001127870.1	P52735-1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
VAV2	ENST00000371850.8 link	c.2136-10_2136-9insGCCCTCACGCAGTGACCGCCGGGGCCGTGTG	intron_variant	1	NM_001134398.2	ENSP00000360916.3	P52735-1
VAV2	ENST00000406606.7 link	c.2106-10_2106-9insGCCCTCACGCAGTGACCGCCGGGGCCGTGTG	intron_variant	1		ENSP00000385362.3	P52735-3
VAV2	ENST00000371851.1 link	c.2106-10_2106-9insGCCCTCACGCAGTGACCGCCGGGGCCGTGTG	intron_variant	5		ENSP00000360917.1	P52735-2

Frequencies

GnomAD3 genomes

AF:

0.353

AC:

53331

AN:

151270

Hom.:

9878

Cov.:

show subpopulations

Gnomad AFR

AF:

0.299

Gnomad AMI

AF:

0.419

Gnomad AMR

AF:

0.322

Gnomad ASJ

AF:

0.344

Gnomad EAS

AF:

0.0427

Gnomad SAS

AF:

0.364

Gnomad FIN

AF:

0.359

Gnomad MID

AF:

0.401

Gnomad NFE

AF:

0.414

Gnomad OTH

AF:

0.354

GnomAD4 exome

AF:

0.387

AC:

560596

AN:

1448216

Hom.:

115689

Cov.:

AF XY:

0.388

AC XY:

279975

AN XY:

720980

show subpopulations

Gnomad4 AFR exome

AF:

0.295

Gnomad4 AMR exome

AF:

0.292

Gnomad4 ASJ exome

AF:

0.334

Gnomad4 EAS exome

AF:

0.0241

Gnomad4 SAS exome

AF:

0.374

Gnomad4 FIN exome

AF:

0.367

Gnomad4 NFE exome

AF:

0.411

Gnomad4 OTH exome

AF:

0.369

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.353

AC:

53370

AN:

151390

Hom.:

9887

Cov.:

AF XY:

0.347

AC XY:

25670

AN XY:

73978

show subpopulations

Gnomad4 AFR

AF:

0.299

Gnomad4 AMR

AF:

0.322

Gnomad4 ASJ

AF:

0.344

Gnomad4 EAS

AF:

0.0428

Gnomad4 SAS

AF:

0.364

Gnomad4 FIN

AF:

0.359

Gnomad4 NFE

AF:

0.414

Gnomad4 OTH

AF:

0.354

Alfa

AF:

0.208

Hom.:

1088

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over