rs9997081

Variant summary

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

The ENST00000512129.2(LEF1-AS1):​n.238+5438T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.867 in 152,138 control chromosomes in the GnomAD database, including 57,475 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 0.87 ( 57475 hom., cov: 31)

Consequence

LEF1-AS1
ENST00000512129.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.659
Variant links:
Genes affected
LEF1-AS1 (HGNC:40339): (LEF1 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.902 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
LEF1-AS1ENST00000512129.2 linkn.238+5438T>A intron_variant Intron 2 of 2 3
LEF1-AS1ENST00000665040.2 linkn.328+5438T>A intron_variant Intron 3 of 3
LEF1-AS1ENST00000693123.1 linkn.451+5438T>A intron_variant Intron 4 of 4

Frequencies

GnomAD3 genomes
AF:
0.868
AC:
131879
AN:
152018
Hom.:
57442
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.769
Gnomad AMI
AF:
0.898
Gnomad AMR
AF:
0.905
Gnomad ASJ
AF:
0.880
Gnomad EAS
AF:
0.869
Gnomad SAS
AF:
0.876
Gnomad FIN
AF:
0.926
Gnomad MID
AF:
0.886
Gnomad NFE
AF:
0.908
Gnomad OTH
AF:
0.855
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.867
AC:
131968
AN:
152138
Hom.:
57475
Cov.:
31
AF XY:
0.868
AC XY:
64589
AN XY:
74382
show subpopulations
Gnomad4 AFR
AF:
0.770
Gnomad4 AMR
AF:
0.904
Gnomad4 ASJ
AF:
0.880
Gnomad4 EAS
AF:
0.868
Gnomad4 SAS
AF:
0.876
Gnomad4 FIN
AF:
0.926
Gnomad4 NFE
AF:
0.908
Gnomad4 OTH
AF:
0.852
Alfa
AF:
0.892
Hom.:
3006
Bravo
AF:
0.861
Asia WGS
AF:
0.851
AC:
2960
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
2.5
DANN
Benign
0.78

Splicing

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: rs9997081; hg19: chr4-109126553; API