rs4984499

Variant names:

• chr15-96104564-T-A
• rs4984499
• ENST00000616608.2:n.575-2341A>T

Your query was ambiguous. Multiple possible variants found:

• chr15-96104564-T-A
• chr15-96104564-T-C
• chr15-96104564-T-G

Variant summary

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

The ENST00000616608.2(NR2F2-AS1):​n.575-2341A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.705 in 151,830 control chromosomes in the GnomAD database, including 38,812 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 0.71 (38812 hom., cov: 30)
• Consequence: NR2F2-AS1 ENST00000616608.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.585
• Publications: 8 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 (AFR) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000616608.2. 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
	LOC105369212	NR_158193.1		n.1087-406A>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NR2F2-AS1	ENST00000616608.2	TSL:5	n.575-2341A>T		intron	N/A
	ENSG00000275443	ENST00000619812.1	TSL:5	n.303+113680T>A		intron	N/A
	NR2F2-AS1	ENST00000742808.1		n.337+14279A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.705 AC: 106928 AN: 151712 Hom.: 38748 Cov.: 30

Gnomad AFR AF: 0.865

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.705 AC: 107059 AN: 151830 Hom.: 38812 Cov.: 30 AF XY: 0.707 AC XY: 52443 AN XY: 74136

African (AFR) AF: 0.865 AC: 35864 AN: 41450

American (AMR) AF: 0.645 AC: 9832 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1738 AN: 3470

East Asian (EAS) AF: 0.857 AC: 4423 AN: 5160

South Asian (SAS) AF: 0.657 AC: 3151 AN: 4794

European-Finnish (FIN) AF: 0.729 AC: 7655 AN: 10500

Middle Eastern (MID) AF: 0.462 AC: 134 AN: 290

European-Non Finnish (NFE) AF: 0.622 AC: 42260 AN: 67910

Other (OTH) AF: 0.649 AC: 1365 AN: 2102

Alfa AF: 0.676 Hom.: 4406

Bravo AF: 0.705

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.6
DANN	Benign	0.70
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs4984499; hg19: chr15-96647793;