rs2398162

Variant names:

• chr15-96287321-A-G
• rs2398162
• ENST00000561344.5:n.396+1343T>C

Variant summary

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

The ENST00000624299.1(NR2F2-AS1):​n.1945T>C 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 0.224 in 152,176 control chromosomes in the GnomAD database, including 4,960 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 0.22 (4960 hom., cov: 33)
  • Exomes 𝑓: 0.14 (0 hom.)
• Consequence: NR2F2-AS1 ENST00000624299.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.781
• Publications: 35 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000624299.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NR2F2-AS1	NR_102743.1		n.409+1343T>C		intron	N/A
	NR2F2-AS1	NR_125738.1		n.317+3309T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NR2F2-AS1	ENST00000561344.5	TSL:1	n.396+1343T>C		intron	N/A
	NR2F2-AS1	ENST00000624299.1	TSL:6	n.1945T>C		non_coding_transcript_exon	Exon 1 of 1
	NR2F2-AS1	ENST00000502125.7	TSL:2	n.339-1862T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34048 AN: 152042 Hom.: 4967 Cov.: 33

Gnomad AFR AF: 0.0830

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.662

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.214

GnomAD4 exome AF: 0.143 AC: 2 AN: 14 Hom.: 0 Cov.: 0 AF XY: 0.200 AC XY: 2 AN XY: 10

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.143 AC: 2 AN: 14

Other (OTH) AC: 0 AN: 0

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.00233887), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.224 AC: 34047 AN: 152162 Hom.: 4960 Cov.: 33 AF XY: 0.234 AC XY: 17369 AN XY: 74382

African (AFR) AF: 0.0828 AC: 3440 AN: 41542

American (AMR) AF: 0.285 AC: 4345 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 705 AN: 3472

East Asian (EAS) AF: 0.662 AC: 3411 AN: 5156

South Asian (SAS) AF: 0.292 AC: 1407 AN: 4826

European-Finnish (FIN) AF: 0.333 AC: 3518 AN: 10572

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16432 AN: 68004

Other (OTH) AF: 0.213 AC: 450 AN: 2112

Alfa AF: 0.236 Hom.: 13780

Bravo AF: 0.218

Asia WGS AF: 0.389 AC: 1352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.66
DANN	Benign	0.76
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs2398162; hg19: chr15-96830550;