Variant chr15-96287321-A-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000624299.1(NR2F2-AS1):n.1945T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 152,176 control chromosomes in the GnomAD database, including 4,960 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 0.22 ( 4960 hom., cov: 33)

Exomes 𝑓: 0.14 ( 0 hom. )

Consequence

NR2F2-AS1
ENST00000624299.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.781

Variant links:

Genes affected

NR2F2-AS1 (HGNC:44222): (NR2F2 antisense RNA 1)

NR2F2-AS1 links:

ENSG00000275443 (HGNC:):

ENSG00000275443 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NR2F2-AS1	NR_102743.1 link	n.409+1343T>C		intron_variant
NR2F2-AS1	NR_125738.1 link	n.317+3309T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
NR2F2-AS1	ENST00000561344.5 link	n.396+1343T>C	intron_variant		1
NR2F2-AS1	ENST00000624299.1 link	n.1945T>C	non_coding_transcript_exon_variant	1/1	6
NR2F2-AS1	ENST00000502125.6 link	n.318-1862T>C	intron_variant		2

Frequencies

GnomAD3 genomes

AF:

0.224

AC:

34048

AN:

152042

Hom.:

4967

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0830

Gnomad AMI

AF:

0.318

Gnomad AMR

AF:

0.284

Gnomad ASJ

AF:

0.203

Gnomad EAS

AF:

0.662

Gnomad SAS

AF:

0.291

Gnomad FIN

AF:

0.333

Gnomad MID

AF:

0.169

Gnomad NFE

AF:

0.242

Gnomad OTH

AF:

0.214

GnomAD4 exome

AF:

0.143

AC:

AN:

Hom.:

Cov.:

AF XY:

0.200

AC XY:

AN XY:

show subpopulations

Gnomad4 NFE exome

AF:

0.143

GnomAD4 genome

AF:

0.224

AC:

34047

AN:

152162

Hom.:

4960

Cov.:

AF XY:

0.234

AC XY:

17369

AN XY:

74382

show subpopulations

Gnomad4 AFR

AF:

0.0828

Gnomad4 AMR

AF:

0.285

Gnomad4 ASJ

AF:

0.203

Gnomad4 EAS

AF:

0.662

Gnomad4 SAS

AF:

0.292

Gnomad4 FIN

AF:

0.333

Gnomad4 NFE

AF:

0.242

Gnomad4 OTH

AF:

0.213

Alfa

AF:

0.244

Hom.:

9162

Bravo

AF:

0.218

Asia WGS

AF:

0.389

AC:

1352

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.66

DANN

Benign

0.76

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over