rs11073474

chr15-96295840-G-Achr15-96295840-G-C

Variant summary

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

The ENST00000623393.1(ENSG00000280291):n.2184C>T variant causes a non coding transcript exon 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: ENST00000623393.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.756

Genes affected

(HGNC:):

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NR2F2-AS1	NR_125738.1	n.164-5057C>T		intron_variant, non_coding_transcript_variant
NR2F2-AS1	NR_102743.1	n.164-5057C>T		intron_variant, non_coding_transcript_variant
NR2F2-AS1	NR_102744.1	n.164-5057C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000623393.1	n.2184C>T		non_coding_transcript_exon_variant	1/1
NR2F2-AS1	ENST00000560800.5	n.67-5057C>T		intron_variant, non_coding_transcript_variant		4
	ENST00000619812.1	n.455-4854G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34469 AN: 151902 Hom.: 5246 Cov.: 32

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: 9 AN: 32 Hom.: 0 Cov.: 0 AF XY: 0.227 AC XY: 5 AN XY: 22

Gnomad4 FIN exome AF: 0.333

Gnomad4 NFE exome AF: 0.269

GnomAD4 genome AF: 0.227 AC: 34464 AN: 152020 Hom.: 5240 Cov.: 32 AF XY: 0.236 AC XY: 17517 AN XY: 74282

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

Other links and lift over

dbSNP: rs11073474; hg19: chr15-96839069;