15-96301498-C-T

Variant names:

• chr15-96301498-C-T
• rs7181753
• ENST00000561344.5:n.151-10715G>A

Variant summary

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

The ENST00000561344.5(NR2F2-AS1):​n.151-10715G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,058 control chromosomes in the GnomAD database, including 4,744 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 0.24 (4744 hom., cov: 32)
• Consequence: NR2F2-AS1 ENST00000561344.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.293
• Publications: 10 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NR2F2-AS1	NR_102743.1	n.164-10715G>A		intron_variant	Intron 1 of 7
NR2F2-AS1	NR_102744.1	n.164-10715G>A		intron_variant	Intron 1 of 1
NR2F2-AS1	NR_125738.1	n.164-10715G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NR2F2-AS1	ENST00000561344.5	n.151-10715G>A		intron_variant	Intron 1 of 6	1
ENSG00000275443	ENST00000743583.1	n.521C>T		non_coding_transcript_exon_variant	Exon 4 of 4
NR2F2-AS1	ENST00000502125.7	n.185-10715G>A		intron_variant	Intron 1 of 5	2

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35901 AN: 151940 Hom.: 4731 Cov.: 32

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.236 AC: 35953 AN: 152058 Hom.: 4744 Cov.: 32 AF XY: 0.235 AC XY: 17453 AN XY: 74322

African (AFR) AF: 0.349 AC: 14462 AN: 41458

American (AMR) AF: 0.227 AC: 3470 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 810 AN: 3470

East Asian (EAS) AF: 0.117 AC: 608 AN: 5176

South Asian (SAS) AF: 0.281 AC: 1352 AN: 4818

European-Finnish (FIN) AF: 0.152 AC: 1598 AN: 10546

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12869 AN: 67978

Other (OTH) AF: 0.227 AC: 479 AN: 2112

Alfa AF: 0.204 Hom.: 8732

Bravo AF: 0.245

Asia WGS AF: 0.199 AC: 690 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.90
DANN	Benign	0.17
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs7181753; hg19: chr15-96844727;