15-96272797-G-C

Position:

• chr15-96272797-G-C

Variant summary

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

The ENST00000558929.5(NR2F2-AS1):​n.573C>G variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.544 in 152,158 control chromosomes in the GnomAD database, including 25,892 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 0.54 (25892 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: NR2F2-AS1 ENST00000558929.5 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.186

Genes affected

NR2F2-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NR2F2-AS1	NR_102743.1	n.702-999C>G		intron_variant
NR2F2-AS1	NR_125738.1	n.317+17833C>G		intron_variant
LOC124903584	XR_007064801.1	n.8852-2186G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NR2F2-AS1	ENST00000561344.5	n.689-999C>G		intron_variant		1
NR2F2-AS1	ENST00000558929.5	n.573C>G		splice_region_variant, non_coding_transcript_exon_variant	5/5	5
NR2F2-AS1	ENST00000560395.5	n.100C>G		non_coding_transcript_exon_variant	2/5	5

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82708 AN: 152038 Hom.: 25884 Cov.: 33

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.557

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.544 AC: 82737 AN: 152158 Hom.: 25892 Cov.: 33 AF XY: 0.544 AC XY: 40500 AN XY: 74408

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.567

Gnomad4 ASJ AF: 0.608

Gnomad4 EAS AF: 0.733

Gnomad4 SAS AF: 0.437

Gnomad4 FIN AF: 0.749

Gnomad4 NFE AF: 0.693

Gnomad4 OTH AF: 0.560

Alfa AF: 0.601 Hom.: 3622

Bravo AF: 0.522

Asia WGS AF: 0.564 AC: 1965 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	14
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11632637; hg19: chr15-96816026;