rs11156352

Variant summary

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

The ENST00000658843.2(UFL1-AS1):​n.302-36631T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,200 control chromosomes in the GnomAD database, including 1,558 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 0.13 ( 1558 hom., cov: 32)

Consequence

UFL1-AS1
ENST00000658843.2 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.437
Variant links:
Genes affected
UFL1-AS1 (HGNC:41007): (UFL1 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=-0.98).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
UFL1-AS1XR_007059687.1 linkuse as main transcriptn.9276-36631T>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
UFL1-AS1ENST00000658843.2 linkuse as main transcriptn.302-36631T>C intron_variant, non_coding_transcript_variant
UFL1-AS1ENST00000662501.1 linkuse as main transcriptn.394-36631T>C intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.130
AC:
19805
AN:
152082
Hom.:
1557
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0842
Gnomad AMI
AF:
0.246
Gnomad AMR
AF:
0.0949
Gnomad ASJ
AF:
0.133
Gnomad EAS
AF:
0.00116
Gnomad SAS
AF:
0.0487
Gnomad FIN
AF:
0.124
Gnomad MID
AF:
0.0696
Gnomad NFE
AF:
0.181
Gnomad OTH
AF:
0.129
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.130
AC:
19808
AN:
152200
Hom.:
1558
Cov.:
32
AF XY:
0.126
AC XY:
9411
AN XY:
74416
show subpopulations
Gnomad4 AFR
AF:
0.0842
Gnomad4 AMR
AF:
0.0947
Gnomad4 ASJ
AF:
0.133
Gnomad4 EAS
AF:
0.00116
Gnomad4 SAS
AF:
0.0477
Gnomad4 FIN
AF:
0.124
Gnomad4 NFE
AF:
0.181
Gnomad4 OTH
AF:
0.127
Alfa
AF:
0.158
Hom.:
721
Bravo
AF:
0.129
Asia WGS
AF:
0.0310
AC:
109
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
1.3
DANN
Benign
0.47

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: rs11156352; hg19: chr6-96687522; API