rs2577001

chr15-96210925-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_125738.1(NR2F2-AS1):n.318-19531G>A variant causes a intron, non coding transcript 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 NR_125738.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
NR2F2-AS1	NR_125738.1	n.318-19531G>A		intron_variant, non_coding_transcript_variant
LOC112268156	XR_002957737.1	n.451-16348C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NR2F2-AS1	ENST00000560800.5	n.221-19531G>A		intron_variant, non_coding_transcript_variant		4
	ENST00000619812.1	n.304-16348C>T		intron_variant, non_coding_transcript_variant		5
NR2F2-AS1	ENST00000559505.1	n.254+11877G>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.223

Alfa AF: 0.209 Hom.: 1797

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2577001; hg19: chr15-96754154;