rs3940231

Positions:

• chr14-24279157-C-T

Variant summary

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

The XM_005267385.2(NOP9):​c.-1342+7847C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 151,956 control chromosomes in the GnomAD database, including 20,669 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 0.50 (20669 hom., cov: 32)
• Consequence: NOP9 XM_005267385.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220

Genes affected

NOP9 (HGNC:19826): (NOP9 nucleolar protein) Enables RNA binding activity. Predicted to be involved in ribosome biogenesis. Predicted to be part of 90S preribosome and preribosome, small subunit precursor. Predicted to be active in nucleolus. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000288044 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NOP9	XM_005267385.2	c.-1342+7847C>T		intron_variant			XP_005267442.1
NOP9	XM_047431052.1	c.-1661+7847C>T		intron_variant			XP_047287008.1
NOP9	XM_047431053.1	c.-1745+7847C>T		intron_variant			XP_047287009.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000288044	ENST00000669726.3	n.110+7847C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75710 AN: 151838 Hom.: 20634 Cov.: 32

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.472

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.499 AC: 75799 AN: 151956 Hom.: 20669 Cov.: 32 AF XY: 0.502 AC XY: 37251 AN XY: 74244

Gnomad4 AFR AF: 0.722

Gnomad4 AMR AF: 0.517

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.594

Gnomad4 SAS AF: 0.585

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.373

Gnomad4 OTH AF: 0.476

Alfa AF: 0.420 Hom.: 7176

Bravo AF: 0.520

Asia WGS AF: 0.607 AC: 2111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.1
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3940231; hg19: chr14-24748363;