rs13017599

Positions:

• chr2-60937196-G-A

Variant summary

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

The ENST00000414613.1(NONOP2):​n.854C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 336,904 control chromosomes in the GnomAD database, including 14,509 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 0.25 (6041 hom., cov: 31)
  • Exomes 𝑓: 0.28 (8468 hom.)
• Consequence: NONOP2 ENST00000414613.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.512

Genes affected

NONOP2 (HGNC:42032): (non-POU domain containing, octamer-binding pseudogene 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NONOP2	ENST00000414613.1	n.854C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.250 AC: 38032 AN: 151986 Hom.: 6044 Cov.: 31

Gnomad AFR AF: 0.0896

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.0164

Gnomad SAS AF: 0.0790

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.269

GnomAD4 exome AF: 0.276 AC: 50971 AN: 184800 Hom.: 8468 Cov.: 0 AF XY: 0.257 AC XY: 26809 AN XY: 104402

Gnomad4 AFR exome AF: 0.0844

Gnomad4 AMR exome AF: 0.207

Gnomad4 ASJ exome AF: 0.273

Gnomad4 EAS exome AF: 0.0239

Gnomad4 SAS exome AF: 0.0920

Gnomad4 FIN exome AF: 0.340

Gnomad4 NFE exome AF: 0.352

Gnomad4 OTH exome AF: 0.276

GnomAD4 genome AF: 0.250 AC: 38020 AN: 152104 Hom.: 6041 Cov.: 31 AF XY: 0.244 AC XY: 18116 AN XY: 74354

Gnomad4 AFR AF: 0.0895

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.288

Gnomad4 EAS AF: 0.0164

Gnomad4 SAS AF: 0.0788

Gnomad4 FIN AF: 0.342

Gnomad4 NFE AF: 0.364

Gnomad4 OTH AF: 0.264

Alfa AF: 0.315 Hom.: 4401

Bravo AF: 0.238

Asia WGS AF: 0.0560 AC: 195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	3.7
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13017599; hg19: chr2-61164331;