chr15-96090647-G-C

Variant names:

• chr15-96090647-G-C
• rs10520807
• ENST00000616608.2:n.713-6000C>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.713-6000C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,150 control chromosomes in the GnomAD database, including 1,718 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 0.10 (1718 hom., cov: 32)
• Consequence: NR2F2-AS1 ENST00000616608.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.362
• Publications: 0 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369212	NR_158193.1	n.1228-6000C>G		intron_variant	Intron 6 of 7
LOC112268156	XR_002957737.1	n.450+99763G>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NR2F2-AS1	ENST00000616608.2	n.713-6000C>G		intron_variant	Intron 7 of 8	5
ENSG00000275443	ENST00000619812.1	n.303+99763G>C		intron_variant	Intron 1 of 3	5
NR2F2-AS1	ENST00000742808.1	n.338-6000C>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15802 AN: 152032 Hom.: 1712 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0869

Gnomad ASJ AF: 0.0622

Gnomad EAS AF: 0.0231

Gnomad SAS AF: 0.0244

Gnomad FIN AF: 0.0335

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0296

Gnomad OTH AF: 0.0947

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

GnomAD4 genome AF: 0.104 AC: 15826 AN: 152150 Hom.: 1718 Cov.: 32 AF XY: 0.103 AC XY: 7651 AN XY: 74394

African (AFR) AF: 0.276 AC: 11439 AN: 41460

American (AMR) AF: 0.0866 AC: 1325 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0622 AC: 216 AN: 3472

East Asian (EAS) AF: 0.0232 AC: 120 AN: 5176

South Asian (SAS) AF: 0.0242 AC: 117 AN: 4826

European-Finnish (FIN) AF: 0.0335 AC: 355 AN: 10594

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0296 AC: 2011 AN: 68006

Other (OTH) AF: 0.0942 AC: 199 AN: 2112

Alfa AF: 0.0774 Hom.: 146

Bravo AF: 0.116

Asia WGS AF: 0.0470 AC: 165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.84
DANN	Benign	0.51
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs10520807; hg19: chr15-96633876;