ENST00000559505.2:n.298-2371A>G

Variant names:

• chr15-96165062-T-C
• rs8023580
• ENST00000559505.2:n.298-2371A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000559505.2(NR2F2-AS1):​n.298-2371A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,100 control chromosomes in the GnomAD database, including 6,651 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 0.29 (6651 hom., cov: 32)
• Consequence: NR2F2-AS1 ENST00000559505.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470
• Publications: 24 publications found

Genes affected

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

ENSG00000275443 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NR2F2-AS1	NR_125738.1	n.360+26290A>G		intron_variant	Intron 3 of 4
LOC112268156	XR_002957737.1	n.451-62211T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NR2F2-AS1	ENST00000559505.2	n.298-2371A>G		intron_variant	Intron 2 of 5	5
NR2F2-AS1	ENST00000560800.5	n.263+26290A>G		intron_variant	Intron 3 of 4	4
NR2F2-AS1	ENST00000616608.2	n.443+26290A>G		intron_variant	Intron 4 of 8	5

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44185 AN: 151980 Hom.: 6646 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.322

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.291 AC: 44219 AN: 152100 Hom.: 6651 Cov.: 32 AF XY: 0.295 AC XY: 21968 AN XY: 74370

African (AFR) AF: 0.248 AC: 10304 AN: 41480

American (AMR) AF: 0.329 AC: 5035 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 1466 AN: 3470

East Asian (EAS) AF: 0.416 AC: 2152 AN: 5172

South Asian (SAS) AF: 0.320 AC: 1541 AN: 4822

European-Finnish (FIN) AF: 0.306 AC: 3239 AN: 10582

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19358 AN: 67966

Other (OTH) AF: 0.319 AC: 674 AN: 2116

Alfa AF: 0.284 Hom.: 16818

Bravo AF: 0.293

Asia WGS AF: 0.329 AC: 1144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.8
DANN	Benign	0.39
PhyloP100		0.047

Splicing

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

Other links and lift over

dbSNP: rs8023580; hg19: chr15-96708291;