dbSNP rs12211125: VNN2:n.*1081A>G (chr6-132743910-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 ENST00000418593.6(VNN2):n.*1081A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0692 in 155,124 control chromosomes in the GnomAD database, including 541 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 0.069 ( 525 hom., cov: 32)

Exomes 𝑓: 0.079 ( 16 hom. )

Consequence

VNN2
ENST00000418593.6 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.358

Publications

7 publications found

Variant links:

Genes affected

VNN2 (HGNC:12706): (vanin 2) This gene product is a member of the Vanin family of proteins that 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. The encoded protein is a GPI-anchored cell surface molecule that plays a role in transendothelial migration of neutrophils. This gene lies in close proximity to, and in same transcriptional orientation as two other vanin genes on chromosome 6q23-q24. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, May 2011]

VNN2 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=-0.88).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VNN2	NM_004665.6 link	c.*390A>G		3_prime_UTR_variant	Exon 7 of 7	ENST00000326499.11	NP_004656.3	O95498-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VNN2	ENST00000326499.11 link	c.*390A>G		3_prime_UTR_variant	Exon 7 of 7	1	NM_004665.6	ENSP00000322276.6		O95498-1

Frequencies

GnomAD3 genomes

AF:

0.0691

AC:

10514

AN:

152128

Hom.:

525

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0170

Gnomad AMI

AF:

0.0471

Gnomad AMR

AF:

0.138

Gnomad ASJ

AF:

0.0985

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.0174

Gnomad FIN

AF:

0.103

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.0872

Gnomad OTH

AF:

0.0855

GnomAD4 exome

AF:

0.0785

AC:

226

AN:

2878

Hom.:

Cov.:

AF XY:

0.0701

AC XY:

105

AN XY:

1498

show subpopulations

African (AFR)

AF:

0.0234

AC:

AN:

128

American (AMR)

AF:

0.140

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.130

AC:

AN:

154

East Asian (EAS)

AF:

0.0132

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.104

AC:

AN:

106

Middle Eastern (MID)

AF:

0.188

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0803

AC:

168

AN:

2092

Other (OTH)

AF:

0.0802

AC:

AN:

162

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.520

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0691

AC:

10515

AN:

152246

Hom.:

525

Cov.:

AF XY:

0.0702

AC XY:

5222

AN XY:

74420

show subpopulations

African (AFR)

AF:

0.0170

AC:

706

AN:

41560

American (AMR)

AF:

0.138

AC:

2113

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0985

AC:

342

AN:

3472

East Asian (EAS)

AF:

0.00135

AC:

AN:

5190

South Asian (SAS)

AF:

0.0172

AC:

AN:

4812

European-Finnish (FIN)

AF:

0.103

AC:

1093

AN:

10584

Middle Eastern (MID)

AF:

0.0510

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0872

AC:

5934

AN:

68016

Other (OTH)

AF:

0.0846

AC:

179

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

488

976

1465

1953

2441

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0834

Hom.:

1040

Bravo

AF:

0.0717

Asia WGS

AF:

0.0140

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.4

(source)

DANN

Benign

0.77

PhyloP100

-0.36

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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rs12211125

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over