7-36819038-A-G

Position:

• chr7-36819038-A-G

Variant summary

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

The ENST00000434232.1(NPM1P18):​n.80A>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 0.492 in 748,004 control chromosomes in the GnomAD database, including 92,741 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 0.46 (17135 hom., cov: 32)
  • Exomes 𝑓: 0.50 (75606 hom.)
• Consequence: NPM1P18 ENST00000434232.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.121

Genes affected

NPM1P18 (HGNC:7920): (nucleophosmin 1 pseudogene 18)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NPM1P18	ENST00000434232.1	n.80A>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70589 AN: 151990 Hom.: 17131 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.442

GnomAD4 exome AF: 0.499 AC: 297532 AN: 595896 Hom.: 75606 Cov.: 3 AF XY: 0.494 AC XY: 160679 AN XY: 325016

Gnomad4 AFR exome AF: 0.337

Gnomad4 AMR exome AF: 0.497

Gnomad4 ASJ exome AF: 0.445

Gnomad4 EAS exome AF: 0.442

Gnomad4 SAS exome AF: 0.397

Gnomad4 FIN exome AF: 0.586

Gnomad4 NFE exome AF: 0.531

Gnomad4 OTH exome AF: 0.479

GnomAD4 genome AF: 0.464 AC: 70627 AN: 152108 Hom.: 17135 Cov.: 32 AF XY: 0.465 AC XY: 34566 AN XY: 74366

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.470

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.606

Gnomad4 NFE AF: 0.533

Gnomad4 OTH AF: 0.438

Alfa AF: 0.508 Hom.: 3475

Bravo AF: 0.451

Asia WGS AF: 0.374 AC: 1301 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	4.8
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10255208; hg19: chr7-36858643;