rs8006081

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014909.5(VASH1):​c.398+540C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.759 in 151,986 control chromosomes in the GnomAD database, including 43,961 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 0.76 ( 43961 hom., cov: 31)

Consequence

VASH1
NM_014909.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.119
Variant links:
Genes affected
VASH1 (HGNC:19964): (vasohibin 1) Enables actin binding activity and metallocarboxypeptidase activity. Involved in negative regulation of angiogenesis; negative regulation of blood vessel endothelial cell migration; and proteolysis. Acts upstream of or within several processes, including negative regulation of endothelial cell migration; negative regulation of endothelial cell proliferation; and negative regulation of lymphangiogenesis. Located in apical part of cell; endoplasmic reticulum; and extracellular space. Implicated in liver cirrhosis and portal hypertension. Biomarker of liver cirrhosis. [provided by Alliance of Genome Resources, Apr 2022]

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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=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
VASH1NM_014909.5 linkuse as main transcriptc.398+540C>T intron_variant ENST00000167106.9 NP_055724.1 Q7L8A9-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
VASH1ENST00000167106.9 linkuse as main transcriptc.398+540C>T intron_variant 1 NM_014909.5 ENSP00000167106.4 Q7L8A9-1
VASH1ENST00000554237.1 linkuse as main transcriptc.398+540C>T intron_variant 1 ENSP00000451613.1 Q7L8A9-2
VASH1ENST00000553518.1 linkuse as main transcriptn.99+540C>T intron_variant 3
VASH1ENST00000556038.5 linkuse as main transcriptn.171+540C>T intron_variant 5

Frequencies

GnomAD3 genomes
AF:
0.758
AC:
115188
AN:
151868
Hom.:
43918
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.781
Gnomad AMI
AF:
0.730
Gnomad AMR
AF:
0.643
Gnomad ASJ
AF:
0.719
Gnomad EAS
AF:
0.681
Gnomad SAS
AF:
0.776
Gnomad FIN
AF:
0.817
Gnomad MID
AF:
0.726
Gnomad NFE
AF:
0.769
Gnomad OTH
AF:
0.750
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.759
AC:
115286
AN:
151986
Hom.:
43961
Cov.:
31
AF XY:
0.759
AC XY:
56397
AN XY:
74264
show subpopulations
Gnomad4 AFR
AF:
0.781
Gnomad4 AMR
AF:
0.643
Gnomad4 ASJ
AF:
0.719
Gnomad4 EAS
AF:
0.682
Gnomad4 SAS
AF:
0.775
Gnomad4 FIN
AF:
0.817
Gnomad4 NFE
AF:
0.769
Gnomad4 OTH
AF:
0.751
Alfa
AF:
0.763
Hom.:
5495
Bravo
AF:
0.743
Asia WGS
AF:
0.717
AC:
2495
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
3.0
DANN
Benign
0.34

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

LitVar

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

Other links and lift over

dbSNP: rs8006081; hg19: chr14-77236934; API