GeneBe

15-96266553-A-T

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000560395.5(NR2F2-AS1):​n.417T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.0 ( 0 hom., cov: 33)
Failed GnomAD Quality Control

Consequence

NR2F2-AS1
ENST00000560395.5 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.198

Publications

6 publications found
Variant links:
Genes affected
NR2F2-AS1 (HGNC:44222): (NR2F2 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NR2F2-AS1NR_102743.1 linkn.983T>A non_coding_transcript_exon_variant Exon 8 of 8
NR2F2-AS1NR_125738.1 linkn.317+24077T>A intron_variant Intron 2 of 4
LOC124903584XR_007064801.1 linkn.8852-8430A>T intron_variant Intron 1 of 1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NR2F2-AS1ENST00000560395.5 linkn.417T>A non_coding_transcript_exon_variant Exon 5 of 5 5
NR2F2-AS1ENST00000561402.6 linkn.906T>A non_coding_transcript_exon_variant Exon 7 of 7 3
NR2F2-AS1ENST00000690325.2 linkn.643T>A non_coding_transcript_exon_variant Exon 5 of 5

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
0
AN:
151968
Hom.:
0
Cov.:
33
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
Cov.:
0
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
151968
Hom.:
0
Cov.:
33
AF XY:
0.00
AC XY:
0
AN XY:
74208
African (AFR)
AF:
0.00
AC:
0
AN:
41390
American (AMR)
AF:
0.00
AC:
0
AN:
15258
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3470
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5188
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4818
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10530
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
67996
Other (OTH)
AF:
0.00
AC:
0
AN:
2090
Alfa
AF:
0.00
Hom.:
31654

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
0.93
DANN
Benign
0.44
PhyloP100
0.20

Splicing

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

Publications

Other links and lift over

dbSNP: rs1437588; hg19: chr15-96809782; API