10-31265249-C-T

Variant summary

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

The ENST00000605946.1(ZEB1-AS1):​n.177+54266G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 151,842 control chromosomes in the GnomAD database, including 6,721 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 0.26 ( 6721 hom., cov: 30)

Consequence

ZEB1-AS1
ENST00000605946.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.98

Publications

1 publications found
Variant links:
Genes affected
ZEB1-AS1 (HGNC:42354): (ZEB1 antisense RNA 1) This locus produces long non-coding RNA that is transcribed from a shared bi-directional promoter with zinc finger E-box binding homeobox 1 (ZEB1). This transcript binds lysine methyltransferase 2A and promotes histone modifications that are thought to promote expression of ZEB1. Expression of this gene is correlated with tumor progression. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2017]

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=-0.93).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZEB1-AS1ENST00000605946.1 linkn.177+54266G>A intron_variant Intron 1 of 1 5
ZEB1-AS1ENST00000805106.1 linkn.202+55034G>A intron_variant Intron 1 of 1

Frequencies

GnomAD3 genomes
AF:
0.261
AC:
39549
AN:
151724
Hom.:
6714
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.0698
Gnomad AMI
AF:
0.591
Gnomad AMR
AF:
0.251
Gnomad ASJ
AF:
0.361
Gnomad EAS
AF:
0.0344
Gnomad SAS
AF:
0.216
Gnomad FIN
AF:
0.297
Gnomad MID
AF:
0.380
Gnomad NFE
AF:
0.383
Gnomad OTH
AF:
0.292
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.261
AC:
39557
AN:
151842
Hom.:
6721
Cov.:
30
AF XY:
0.254
AC XY:
18828
AN XY:
74170
show subpopulations
African (AFR)
AF:
0.0696
AC:
2886
AN:
41460
American (AMR)
AF:
0.252
AC:
3842
AN:
15260
Ashkenazi Jewish (ASJ)
AF:
0.361
AC:
1253
AN:
3468
East Asian (EAS)
AF:
0.0345
AC:
178
AN:
5156
South Asian (SAS)
AF:
0.216
AC:
1041
AN:
4810
European-Finnish (FIN)
AF:
0.297
AC:
3113
AN:
10496
Middle Eastern (MID)
AF:
0.388
AC:
114
AN:
294
European-Non Finnish (NFE)
AF:
0.383
AC:
25986
AN:
67896
Other (OTH)
AF:
0.290
AC:
607
AN:
2094
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.508
Heterozygous variant carriers
0
1327
2654
3980
5307
6634
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
392
784
1176
1568
1960
<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:
0.321
Hom.:
8242
Bravo
AF:
0.250

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.048
DANN
Benign
0.26
PhyloP100
-3.0

Splicing

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

Publications

Other links and lift over

dbSNP: rs7083727; hg19: chr10-31554178; API