Genetic Variant NR2F2-AS1:n.151-5057C>T (chr15-96295840-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -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

Publications

3 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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	ENST00000502125.7 link	n.185-5057C>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

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.333

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.269

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.547

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.227

AC:

34464

AN:

152020

Hom.:

5240

Cov.:

AF XY:

0.236

AC XY:

17517

AN XY:

74282

show subpopulations

African (AFR)

AF:

0.0620

AC:

2576

AN:

41518

American (AMR)

AF:

0.291

AC:

4447

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.213

AC:

739

AN:

3470

East Asian (EAS)

AF:

0.664

AC:

3424

AN:

5156

South Asian (SAS)

AF:

0.292

AC:

1406

AN:

4816

European-Finnish (FIN)

AF:

0.327

AC:

3450

AN:

10546

Middle Eastern (MID)

AF:

0.163

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.260

AC:

17666

AN:

67936

Other (OTH)

AF:

0.224

AC:

471

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1239

2478

3718

4957

6196

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

372

744

1116

1488

1860

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.217

Hom.:

3073

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

(source)

DANN

Benign

0.65

PhyloP100

-0.76

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over