Genetic Variant ENST00000561344.5:n.151-5057C>T (chr15-96295840-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000561344.5(NR2F2-AS1):n.151-5057C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 152,052 control chromosomes in the GnomAD database, including 5,240 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 0.23 ( 5240 hom., cov: 32)

Exomes 𝑓: 0.28 ( 0 hom. )

Consequence

NR2F2-AS1
ENST00000561344.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.756

Variant links:

Genes affected

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

NR2F2-AS1 links:

ENSG00000280291 (HGNC:):

ENSG00000280291 links:

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=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
NR2F2-AS1	NR_102743.1 link	n.164-5057C>T	intron_variant	Intron 1 of 7
NR2F2-AS1	NR_102744.1 link	n.164-5057C>T	intron_variant	Intron 1 of 1
NR2F2-AS1	NR_125738.1 link	n.164-5057C>T	intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
NR2F2-AS1	ENST00000561344.5 link	n.151-5057C>T	intron_variant	Intron 1 of 6	1
ENSG00000280291	ENST00000623393.1 link	n.2184C>T	non_coding_transcript_exon_variant	Exon 1 of 1	6
NR2F2-AS1	ENST00000502125.6 link	n.164-5057C>T	intron_variant	Intron 1 of 5	2

Frequencies

GnomAD3 genomes

AF:

0.227

AC:

34469

AN:

151902

Hom.:

5246

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0622

Gnomad AMI

AF:

0.260

Gnomad AMR

AF:

0.291

Gnomad ASJ

AF:

0.213

Gnomad EAS

AF:

0.664

Gnomad SAS

AF:

0.291

Gnomad FIN

AF:

0.327

Gnomad MID

AF:

0.168

Gnomad NFE

AF:

0.260

Gnomad OTH

AF:

0.225

GnomAD4 exome

AF:

0.281

AC:

AN:

Hom.:

Cov.:

AF XY:

0.227

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

0.333

Gnomad4 NFE exome

AF:

0.269

GnomAD4 genome

AF:

0.227

AC:

34464

AN:

152020

Hom.:

5240

Cov.:

AF XY:

0.236

AC XY:

17517

AN XY:

74282

show subpopulations

Gnomad4 AFR

AF:

0.0620

Gnomad4 AMR

AF:

0.291

Gnomad4 ASJ

AF:

0.213

Gnomad4 EAS

AF:

0.664

Gnomad4 SAS

AF:

0.292

Gnomad4 FIN

AF:

0.327

Gnomad4 NFE

AF:

0.260

Gnomad4 OTH

AF:

0.224

Alfa

AF:

0.246

Hom.:

1461

Bravo

AF:

0.219

Asia WGS

AF:

0.387

AC:

1344

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.20

DANN

Benign

0.65

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