6-132743910-T-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004665.6(VNN2):c.*390A>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 0.0692 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
NM_004665.6 3_prime_UTR
NM_004665.6 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.358
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VNN2 | NM_004665.6 | c.*390A>G | 3_prime_UTR_variant | 7/7 | ENST00000326499.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VNN2 | ENST00000326499.11 | c.*390A>G | 3_prime_UTR_variant | 7/7 | 1 | NM_004665.6 | P1 | ||
VNN2 | ENST00000418593.6 | c.*1081A>G | 3_prime_UTR_variant, NMD_transcript_variant | 7/7 | 1 | ||||
VNN2 | ENST00000422400.6 | c.*1207A>G | 3_prime_UTR_variant, NMD_transcript_variant | 8/8 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0691 AC: 10514AN: 152128Hom.: 525 Cov.: 32
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GnomAD4 exome AF: 0.0785 AC: 226AN: 2878Hom.: 16 Cov.: 0 AF XY: 0.0701 AC XY: 105AN XY: 1498
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GnomAD4 genome ? AF: 0.0691 AC: 10515AN: 152246Hom.: 525 Cov.: 32 AF XY: 0.0702 AC XY: 5222AN XY: 74420
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at