rs11073474

Variant names:

• chr15-96295840-G-A
• rs11073474
• ENST00000561344.5:n.151-5057C>T

Your query was ambiguous. Multiple possible variants found:

• chr15-96295840-G-A
• chr15-96295840-G-C

Variant summary

Our verdict is Benign. The variant received -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: ENSG00000280291 ENST00000623393.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.756
• Publications: 3 publications found

Genes affected

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

ENSG00000280291 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000623393.1. 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.164-5057C>T		intron	N/A
	NR2F2-AS1	NR_102744.1		n.164-5057C>T		intron	N/A
	NR2F2-AS1	NR_125738.1		n.164-5057C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NR2F2-AS1	ENST00000561344.5	TSL:1	n.151-5057C>T		intron	N/A
	ENSG00000280291	ENST00000623393.1	TSL:6	n.2184C>T		non_coding_transcript_exon	Exon 1 of 1
	NR2F2-AS1	ENST00000502125.7	TSL:2	n.185-5057C>T		intron	N/A

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

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) AF: 0.333 AC: 2 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.269 AC: 7 AN: 26

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.0620 AC: 2576 AN: 41518

American (AMR) AF: 0.291 AC: 4447 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 739 AN: 3470

East Asian (EAS) AF: 0.664 AC: 3424 AN: 5156

South Asian (SAS) AF: 0.292 AC: 1406 AN: 4816

European-Finnish (FIN) AF: 0.327 AC: 3450 AN: 10546

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17666 AN: 67936

Other (OTH) AF: 0.224 AC: 471 AN: 2104

Alfa AF: 0.217 Hom.: 3073

Bravo AF: 0.219

Asia WGS AF: 0.387 AC: 1344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.20
DANN	Benign	0.65
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs11073474; hg19: chr15-96839069;