rs8097810

Variant names:

• chr18-26205684-A-G
• rs8097810
• ENST00000578162.1:n.647A>G

Your query was ambiguous. Multiple possible variants found:

• chr18-26205684-A-G
• chr18-26205684-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
NPM1P2		n.26205684A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NPM1P2	ENST00000578162.1	n.647A>G		non_coding_transcript_exon_variant	Exon 3 of 3	6

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

African (AFR) AF: 0.195 AC: 1159 AN: 5946

American (AMR) AF: 0.204 AC: 2506 AN: 12296

Ashkenazi Jewish (ASJ) AF: 0.0660 AC: 430 AN: 6520

East Asian (EAS) AF: 0.143 AC: 1447 AN: 10098

South Asian (SAS) AF: 0.0781 AC: 3377 AN: 43220

European-Finnish (FIN) AF: 0.0850 AC: 814 AN: 9578

Middle Eastern (MID) AF: 0.0466 AC: 40 AN: 858

European-Non Finnish (NFE) AF: 0.0598 AC: 8201 AN: 137134

Other (OTH) AF: 0.0855 AC: 985 AN: 11526

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

African (AFR) AF: 0.202 AC: 8378 AN: 41518

American (AMR) AF: 0.165 AC: 2528 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0764 AC: 265 AN: 3470

East Asian (EAS) AF: 0.148 AC: 769 AN: 5184

South Asian (SAS) AF: 0.0917 AC: 442 AN: 4822

European-Finnish (FIN) AF: 0.0807 AC: 856 AN: 10610

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0618 AC: 4207 AN: 68024

Other (OTH) AF: 0.110 AC: 233 AN: 2114

Alfa AF: 0.0834 Hom.: 863

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
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs8097810; hg19: chr18-23785648;