rs7181753

chr15-96301498-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_125738.1(NR2F2-AS1):n.164-10715G>A variant causes a intron, non coding transcript 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 NR_125738.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.293

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
NR2F2-AS1	NR_125738.1	n.164-10715G>A		intron_variant, non_coding_transcript_variant
NR2F2-AS1	NR_102743.1	n.164-10715G>A		intron_variant, non_coding_transcript_variant
NR2F2-AS1	NR_102744.1	n.164-10715G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NR2F2-AS1	ENST00000560800.5	n.67-10715G>A		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.117

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.227

Alfa AF: 0.195 Hom.: 4983

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7181753; hg19: chr15-96844727;