rs8097810

chr18-26205684-A-G

Variant summary

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

The ENST00000578162.1(NPM1P2):n.647A>G 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 0.0942 in 389,408 control chromosomes in the GnomAD database, including 2,465 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 0.12 (1438 hom., cov: 32)
  • Exomes 𝑓: 0.080 (1027 hom.)
• Consequence: NPM1P2 ENST00000578162.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.678

Genes affected

NPM1P2 (HGNC:7922): (nucleophosmin 1 pseudogene 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.198 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
NPM1P2	ENST00000578162.1	n.647A>G		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17703 AN: 152114 Hom.: 1430 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.0764

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.0918

Gnomad FIN AF: 0.0807

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0619

Gnomad OTH AF: 0.111

GnomAD4 exome AF: 0.0799 AC: 18959 AN: 237176 Hom.: 1027 Cov.: 0 AF XY: 0.0773 AC XY: 10526 AN XY: 136240

Gnomad4 AFR exome AF: 0.195

Gnomad4 AMR exome AF: 0.204

Gnomad4 ASJ exome AF: 0.0660

Gnomad4 EAS exome AF: 0.143

Gnomad4 SAS exome AF: 0.0781

Gnomad4 FIN exome AF: 0.0850

Gnomad4 NFE exome AF: 0.0598

Gnomad4 OTH exome AF: 0.0855

GnomAD4 genome AF: 0.117 AC: 17742 AN: 152232 Hom.: 1438 Cov.: 32 AF XY: 0.117 AC XY: 8678 AN XY: 74438

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.0764

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.0917

Gnomad4 FIN AF: 0.0807

Gnomad4 NFE AF: 0.0618

Gnomad4 OTH AF: 0.110

Alfa AF: 0.0769 Hom.: 581

Bravo AF: 0.131

Asia WGS AF: 0.146 AC: 506 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	2.4
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8097810; hg19: chr18-23785648;