7-36819038-A-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NPM1P18		n.36819038A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NPM1P18	ENST00000434232.1	n.80A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000230831	ENST00000829529.1	n.743-21945A>G		intron_variant	Intron 1 of 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

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 v4.3

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;