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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000414613.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NONOP2	ENST00000414613.1	TSL:6	n.854C>T		non_coding_transcript_exon	Exon 1 of 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

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs13017599;

hg19: chr2-61164331;