chr15-96274238-C-A

Variant names:

• chr15-96274238-C-A
• rs7182413
• ENST00000561344.5:n.689-2440G>T

Variant summary

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

The ENST00000561344.5(NR2F2-AS1):​n.689-2440G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.633 in 152,072 control chromosomes in the GnomAD database, including 31,254 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 0.63 (31254 hom., cov: 33)
• Consequence: NR2F2-AS1 ENST00000561344.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124
• Publications: 6 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NR2F2-AS1	NR_102743.1	n.702-2440G>T		intron_variant	Intron 5 of 7
NR2F2-AS1	NR_125738.1	n.317+16392G>T		intron_variant	Intron 2 of 4
LOC124903584	XR_007064801.1	n.8852-745C>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NR2F2-AS1	ENST00000561344.5	n.689-2440G>T		intron_variant	Intron 5 of 6	1
NR2F2-AS1	ENST00000502125.7	n.631-2440G>T		intron_variant	Intron 4 of 5	2
NR2F2-AS1	ENST00000557863.7	n.626+8594G>T		intron_variant	Intron 4 of 4	3

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96138 AN: 151954 Hom.: 31235 Cov.: 33

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.838

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.744

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.633 AC: 96212 AN: 152072 Hom.: 31254 Cov.: 33 AF XY: 0.635 AC XY: 47217 AN XY: 74354

African (AFR) AF: 0.492 AC: 20400 AN: 41468

American (AMR) AF: 0.683 AC: 10432 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.661 AC: 2296 AN: 3472

East Asian (EAS) AF: 0.837 AC: 4317 AN: 5156

South Asian (SAS) AF: 0.521 AC: 2508 AN: 4818

European-Finnish (FIN) AF: 0.744 AC: 7867 AN: 10578

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.680 AC: 46231 AN: 67980

Other (OTH) AF: 0.645 AC: 1363 AN: 2114

Alfa AF: 0.662 Hom.: 20773

Bravo AF: 0.629

Asia WGS AF: 0.674 AC: 2345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.8
DANN	Benign	0.85
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs7182413; hg19: chr15-96817467;