15-96155245-G-T

Position:

• chr15-96155245-G-T

Variant summary

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

The ENST00000560800.5(NR2F2-AS1):​n.264-23183C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.754 in 152,146 control chromosomes in the GnomAD database, including 43,352 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 0.75 (43352 hom., cov: 33)
• Consequence: NR2F2-AS1 ENST00000560800.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295

Genes affected

NR2F2-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NR2F2-AS1	NR_125738.1	n.361-23183C>A		intron_variant
LOC112268156	XR_002957737.1	n.451-72028G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NR2F2-AS1	ENST00000559505.1	n.809+1241C>A		intron_variant		5
NR2F2-AS1	ENST00000560800.5	n.264-23183C>A		intron_variant		4
ENSG00000275443	ENST00000619812.1	n.304-72028G>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.754 AC: 114568 AN: 152028 Hom.: 43310 Cov.: 33

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.835

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.763

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

GnomAD4 genome AF: 0.754 AC: 114667 AN: 152146 Hom.: 43352 Cov.: 33 AF XY: 0.750 AC XY: 55784 AN XY: 74372

Gnomad4 AFR AF: 0.767

Gnomad4 AMR AF: 0.708

Gnomad4 ASJ AF: 0.835

Gnomad4 EAS AF: 0.886

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.734

Gnomad4 NFE AF: 0.753

Gnomad4 OTH AF: 0.766

Alfa AF: 0.741 Hom.: 8445

Bravo AF: 0.756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.3
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs727896; hg19: chr15-96698474;