15-96272797-G-C

Variant names:

• chr15-96272797-G-C
• rs11632637
• ENST00000561344.5:n.689-999C>G

Variant summary

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

The ENST00000561344.5(NR2F2-AS1):​n.689-999C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.544 in 152,158 control chromosomes in the GnomAD database, including 25,892 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 0.54 (25892 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: NR2F2-AS1 ENST00000561344.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.186
• Publications: 3 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 = 0.714 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000561344.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NR2F2-AS1	NR_102743.1		n.702-999C>G		intron	N/A
	NR2F2-AS1	NR_125738.1		n.317+17833C>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NR2F2-AS1	ENST00000561344.5	TSL:1	n.689-999C>G		intron	N/A
	NR2F2-AS1	ENST00000558929.6	TSL:5	n.573C>G		non_coding_transcript_exon	Exon 5 of 9
	NR2F2-AS1	ENST00000560395.5	TSL:5	n.100C>G		non_coding_transcript_exon	Exon 2 of 5

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82708 AN: 152038 Hom.: 25884 Cov.: 33

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.557

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

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) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.544 AC: 82737 AN: 152158 Hom.: 25892 Cov.: 33 AF XY: 0.544 AC XY: 40500 AN XY: 74408

African (AFR) AF: 0.218 AC: 9059 AN: 41506

American (AMR) AF: 0.567 AC: 8672 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2107 AN: 3466

East Asian (EAS) AF: 0.733 AC: 3795 AN: 5174

South Asian (SAS) AF: 0.437 AC: 2105 AN: 4820

European-Finnish (FIN) AF: 0.749 AC: 7930 AN: 10582

Middle Eastern (MID) AF: 0.545 AC: 159 AN: 292

European-Non Finnish (NFE) AF: 0.693 AC: 47105 AN: 68004

Other (OTH) AF: 0.560 AC: 1185 AN: 2116

Alfa AF: 0.601 Hom.: 3622

Bravo AF: 0.522

Asia WGS AF: 0.564 AC: 1965 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	14
DANN	Benign	0.70
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs11632637; hg19: chr15-96816026;