chr15-96210925-C-T

Variant names:

• chr15-96210925-C-T
• rs2577001
• ENST00000559505.2:n.254+11877G>A

Variant summary

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

The ENST00000559505.2(NR2F2-AS1):​n.254+11877G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 151,942 control chromosomes in the GnomAD database, including 3,658 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 0.21 (3658 hom., cov: 32)
• Consequence: NR2F2-AS1 ENST00000559505.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NR2F2-AS1	NR_125738.1	n.318-19531G>A		intron_variant	Intron 2 of 4
LOC112268156	XR_002957737.1	n.451-16348C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NR2F2-AS1	ENST00000559505.2	n.254+11877G>A		intron_variant	Intron 1 of 5	5
NR2F2-AS1	ENST00000560800.5	n.221-19531G>A		intron_variant	Intron 2 of 4	4
NR2F2-AS1	ENST00000616608.2	n.401-19531G>A		intron_variant	Intron 3 of 8	5

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32185 AN: 151824 Hom.: 3666 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.212 AC: 32184 AN: 151942 Hom.: 3658 Cov.: 32 AF XY: 0.214 AC XY: 15907 AN XY: 74276

African (AFR) AF: 0.206 AC: 8544 AN: 41408

American (AMR) AF: 0.231 AC: 3528 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 661 AN: 3468

East Asian (EAS) AF: 0.386 AC: 1991 AN: 5160

South Asian (SAS) AF: 0.384 AC: 1844 AN: 4798

European-Finnish (FIN) AF: 0.140 AC: 1478 AN: 10562

Middle Eastern (MID) AF: 0.223 AC: 65 AN: 292

European-Non Finnish (NFE) AF: 0.196 AC: 13347 AN: 67968

Other (OTH) AF: 0.223 AC: 469 AN: 2106

Alfa AF: 0.208 Hom.: 1965

Bravo AF: 0.218

Asia WGS AF: 0.348 AC: 1205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.2
DANN	Benign	0.57
PhyloP100		0.014

Splicing

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

Other links and lift over

dbSNP: rs2577001; hg19: chr15-96754154;