dbSNP rs4897612: VNN1:c.-151T>G (chr6-132714186-A-C) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_004666.3(VNN1):c.-151T>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 683,500 control chromosomes in the GnomAD database, including 64,653 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.52 ( 23806 hom., cov: 32)

Exomes 𝑓: 0.38 ( 40847 hom. )

Consequence

VNN1
NM_004666.3 upstream_gene

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -2.25

Variant links:

Genes affected

VNN1 (HGNC:12705): (vanin 1) This gene encodes a member of the vanin family of proteins, which share extensive sequence similarity with each other, and also with biotinidase. The family includes secreted and membrane-associated proteins, a few of which have been reported to participate in hematopoietic cell trafficking. No biotinidase activity has been demonstrated for any of the vanin proteins, however, they possess pantetheinase activity, which may play a role in oxidative-stress response. This protein, like its mouse homolog, is likely a GPI-anchored cell surface molecule. The mouse protein is expressed by the perivascular thymic stromal cells and regulates migration of T-cell progenitors to the thymus. This gene lies in close proximity to, and in the same transcriptional orientation as, two other vanin genes on chromosome 6q23-q24. [provided by RefSeq, Feb 2009]

VNN1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 6-132714186-A-C is Benign according to our data. Variant chr6-132714186-A-C is described in ClinVar as [Benign]. Clinvar id is 6230.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.838 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VNN1	NM_004666.3 link	c.-151T>G		upstream_gene_variant		ENST00000367928.5	NP_004657.2	O95497

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VNN1	ENST00000367928.5 link	c.-151T>G		upstream_gene_variant		1	NM_004666.3	ENSP00000356905.4		O95497

Frequencies

GnomAD3 genomes

AF:

0.515

AC:

78327

AN:

151988

Hom.:

23755

Cov.:

show subpopulations

Gnomad AFR

AF:

0.845

Gnomad AMI

AF:

0.313

Gnomad AMR

AF:

0.553

Gnomad ASJ

AF:

0.301

Gnomad EAS

AF:

0.382

Gnomad SAS

AF:

0.472

Gnomad FIN

AF:

0.430

Gnomad MID

AF:

0.369

Gnomad NFE

AF:

0.347

Gnomad OTH

AF:

0.508

GnomAD4 exome

AF:

0.376

AC:

199819

AN:

531394

Hom.:

40847

AF XY:

0.378

AC XY:

104347

AN XY:

275692

show subpopulations

Gnomad4 AFR exome

AF:

0.841

Gnomad4 AMR exome

AF:

0.563

Gnomad4 ASJ exome

AF:

0.308

Gnomad4 EAS exome

AF:

0.371

Gnomad4 SAS exome

AF:

0.456

Gnomad4 FIN exome

AF:

0.409

Gnomad4 NFE exome

AF:

0.336

Gnomad4 OTH exome

AF:

0.399

GnomAD4 genome

AF:

0.516

AC:

78445

AN:

152106

Hom.:

23806

Cov.:

AF XY:

0.519

AC XY:

38596

AN XY:

74342

show subpopulations

Gnomad4 AFR

AF:

0.845

Gnomad4 AMR

AF:

0.552

Gnomad4 ASJ

AF:

0.301

Gnomad4 EAS

AF:

0.383

Gnomad4 SAS

AF:

0.473

Gnomad4 FIN

AF:

0.430

Gnomad4 NFE

AF:

0.347

Gnomad4 OTH

AF:

0.510

Alfa

AF:

0.492

Hom.:

3910

Bravo

AF:

0.537

Asia WGS

AF:

0.512

AC:

1784

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

RECLASSIFIED - VNN1 POLYMORPHISM

Benign:1

Oct 01, 2007

OMIM

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.34

DANN

Benign

0.53

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