rs13017599

Variant names:

• chr2-60937196-G-A
• rs13017599
• ENST00000414613.1:n.854C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 64 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
NONOP2		n.60937196G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NONOP2	ENST00000414613.1	n.854C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

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

African (AFR) AF: 0.0844 AC: 291 AN: 3446

American (AMR) AF: 0.207 AC: 1696 AN: 8184

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 930 AN: 3402

East Asian (EAS) AF: 0.0239 AC: 124 AN: 5196

South Asian (SAS) AF: 0.0920 AC: 3147 AN: 34208

European-Finnish (FIN) AF: 0.340 AC: 7207 AN: 21176

Middle Eastern (MID) AF: 0.191 AC: 261 AN: 1370

European-Non Finnish (NFE) AF: 0.352 AC: 34940 AN: 99226

Other (OTH) AF: 0.276 AC: 2375 AN: 8592

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

African (AFR) AF: 0.0895 AC: 3716 AN: 41510

American (AMR) AF: 0.232 AC: 3538 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 998 AN: 3468

East Asian (EAS) AF: 0.0164 AC: 85 AN: 5172

South Asian (SAS) AF: 0.0788 AC: 380 AN: 4820

European-Finnish (FIN) AF: 0.342 AC: 3619 AN: 10580

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.364 AC: 24753 AN: 67952

Other (OTH) AF: 0.264 AC: 559 AN: 2114

Alfa AF: 0.310 Hom.: 16977

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
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs13017599; hg19: chr2-61164331;