rs766716

Variant names:

• chr15-96145141-T-C
• rs766716
• ENST00000560800.5:n.264-13079A>G

Your query was ambiguous. Multiple possible variants found:

• chr15-96145141-T-C
• chr15-96145141-T-G

Variant summary

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

The ENST00000560800.5(NR2F2-AS1):​n.264-13079A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,096 control chromosomes in the GnomAD database, including 2,949 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 0.19 (2949 hom., cov: 32)
• Consequence: NR2F2-AS1 ENST00000560800.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

Genes affected

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

ENSG00000275443 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NR2F2-AS1	NR_125738.1	n.361-13079A>G		intron_variant	Intron 3 of 4
LOC112268156	XR_002957737.1	n.451-82132T>C		intron_variant	Intron 1 of 1
LOC124903583	XR_007064800.1	n.91-2211A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NR2F2-AS1	ENST00000560800.5	n.264-13079A>G		intron_variant	Intron 3 of 4	4
ENSG00000275443	ENST00000619812.1	n.304-82132T>C		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29181 AN: 151978 Hom.: 2947 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.192 AC: 29182 AN: 152096 Hom.: 2949 Cov.: 32 AF XY: 0.192 AC XY: 14287 AN XY: 74328

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.213

Alfa AF: 0.205 Hom.: 2520

Bravo AF: 0.186

Asia WGS AF: 0.208 AC: 722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.34
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs766716; hg19: chr15-96688370;