GeneBe

rs1470379

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000437232.5(VIM-AS1):​n.118-526G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 152,036 control chromosomes in the GnomAD database, including 5,470 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 0.25 ( 5470 hom., cov: 32)

Consequence

VIM-AS1
ENST00000437232.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.04

Publications

7 publications found
Variant links:
Genes affected
VIM-AS1 (HGNC:44879): (VIM antisense RNA 1)

Genome browser will be placed here

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=-0.64).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
VIM-AS1NR_108060.1 linkn.118-526G>A intron_variant Intron 2 of 3
VIM-AS1NR_108061.1 linkn.642-526G>A intron_variant Intron 1 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
VIM-AS1ENST00000437232.5 linkn.118-526G>A intron_variant Intron 2 of 3 2
VIM-AS1ENST00000605833.3 linkn.686-526G>A intron_variant Intron 1 of 2 3
VIM-AS1ENST00000661048.2 linkn.479-1436G>A intron_variant Intron 1 of 1

Frequencies

GnomAD3 genomes
AF:
0.247
AC:
37528
AN:
151918
Hom.:
5460
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0892
Gnomad AMI
AF:
0.431
Gnomad AMR
AF:
0.365
Gnomad ASJ
AF:
0.182
Gnomad EAS
AF:
0.284
Gnomad SAS
AF:
0.180
Gnomad FIN
AF:
0.342
Gnomad MID
AF:
0.203
Gnomad NFE
AF:
0.305
Gnomad OTH
AF:
0.251
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.247
AC:
37545
AN:
152036
Hom.:
5470
Cov.:
32
AF XY:
0.249
AC XY:
18505
AN XY:
74302
show subpopulations
African (AFR)
AF:
0.0890
AC:
3692
AN:
41494
American (AMR)
AF:
0.366
AC:
5591
AN:
15276
Ashkenazi Jewish (ASJ)
AF:
0.182
AC:
632
AN:
3470
East Asian (EAS)
AF:
0.284
AC:
1461
AN:
5150
South Asian (SAS)
AF:
0.181
AC:
871
AN:
4824
European-Finnish (FIN)
AF:
0.342
AC:
3610
AN:
10556
Middle Eastern (MID)
AF:
0.197
AC:
58
AN:
294
European-Non Finnish (NFE)
AF:
0.305
AC:
20701
AN:
67946
Other (OTH)
AF:
0.254
AC:
536
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1378
2756
4134
5512
6890
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
378
756
1134
1512
1890
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.286
Hom.:
4729
Bravo
AF:
0.246
Asia WGS
AF:
0.249
AC:
864
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.64
CADD
Benign
1.3
DANN
Benign
0.91
PhyloP100
-1.0

Splicing

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

Publications

Other links and lift over

dbSNP: rs1470379; hg19: chr10-17258799; API