GeneBe

rs1366818216

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001301056.2(VASH2):​c.181C>A​(p.His61Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H61Y) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

VASH2
NM_001301056.2 missense

Scores

3
15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.51

Publications

0 publications found
Variant links:
Genes affected
VASH2 (HGNC:25723): (vasohibin 2) Enables actin binding activity; metallocarboxypeptidase activity; and microtubule binding activity. Involved in axon development and proteolysis. Acts upstream of or within cell-cell fusion; positive regulation of angiogenesis; and positive regulation of endothelial cell proliferation. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.09888455).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001301056.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
VASH2
NM_001301056.2
MANE Select
c.181C>Ap.His61Asn
missense
Exon 2 of 8NP_001287985.1Q86V25-1
VASH2
NM_024749.5
c.181C>Ap.His61Asn
missense
Exon 2 of 6NP_079025.2
VASH2
NM_001136474.3
c.-15C>A
5_prime_UTR
Exon 3 of 9NP_001129946.1Q86V25-2

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
VASH2
ENST00000517399.3
TSL:1 MANE Select
c.181C>Ap.His61Asn
missense
Exon 2 of 8ENSP00000428324.1Q86V25-1
VASH2
ENST00000366965.6
TSL:1
c.181C>Ap.His61Asn
missense
Exon 2 of 6ENSP00000355932.2Q86V25-5
VASH2
ENST00000917486.1
c.181C>Ap.His61Asn
missense
Exon 2 of 7ENSP00000587545.1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD2 exomes
AF:
0.00
AC:
0
AN:
231904
AF XY:
0.00
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Cov.:
33
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.060
BayesDel_addAF
Benign
-0.20
T
BayesDel_noAF
Benign
-0.53
CADD
Benign
23
DANN
Benign
0.97
DEOGEN2
Benign
0.035
T
Eigen
Benign
0.045
Eigen_PC
Benign
0.17
FATHMM_MKL
Uncertain
0.78
D
LIST_S2
Uncertain
0.88
D
M_CAP
Benign
0.045
D
MetaRNN
Benign
0.099
T
MetaSVM
Benign
-0.87
T
MutationAssessor
Benign
0.69
N
PhyloP100
3.5
PrimateAI
Uncertain
0.73
T
PROVEAN
Benign
-0.63
N
REVEL
Benign
0.052
Sift
Benign
0.24
T
Sift4G
Benign
0.27
T
Polyphen
0.37
B
Vest4
0.31
MutPred
0.26
Gain of MoRF binding (P = 0.0879)
MVP
0.068
MPC
0.39
ClinPred
0.46
T
GERP RS
4.7
Varity_R
0.37
gMVP
0.21
Mutation Taster
=76/24
polymorphism

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs1366818216; hg19: chr1-213125065; COSMIC: COSV55117526; API