ENST00000434232.1:n.80A>G

Variant names:

• chr7-36819038-A-G
• rs10255208
• ENST00000434232.1:n.80A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

Genes affected

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

ENSG00000230831 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000434232.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPM1P18	ENST00000434232.1	TSL:6	n.80A>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000230831	ENST00000829529.1		n.743-21945A>G		intron	N/A

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

African (AFR) AF: 0.337 AC: 5828 AN: 17286

American (AMR) AF: 0.497 AC: 21097 AN: 42406

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 9038 AN: 20328

East Asian (EAS) AF: 0.442 AC: 15753 AN: 35640

South Asian (SAS) AF: 0.397 AC: 26843 AN: 67622

European-Finnish (FIN) AF: 0.586 AC: 21663 AN: 36962

Middle Eastern (MID) AF: 0.392 AC: 959 AN: 2448

European-Non Finnish (NFE) AF: 0.531 AC: 180968 AN: 341094

Other (OTH) AF: 0.479 AC: 15383 AN: 32110

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

African (AFR) AF: 0.339 AC: 14050 AN: 41482

American (AMR) AF: 0.424 AC: 6477 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1585 AN: 3472

East Asian (EAS) AF: 0.470 AC: 2432 AN: 5178

South Asian (SAS) AF: 0.400 AC: 1928 AN: 4816

European-Finnish (FIN) AF: 0.606 AC: 6412 AN: 10576

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.533 AC: 36233 AN: 67986

Other (OTH) AF: 0.438 AC: 923 AN: 2108

Alfa AF: 0.503 Hom.: 3527

Bravo AF: 0.451

Asia WGS AF: 0.374 AC: 1301 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	4.8
DANN	Benign	0.52
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs10255208; hg19: chr7-36858643;