chr14-24282528-C-A

Position:

• chr14-24282528-C-A

Variant summary

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

The XM_005267385.2(NOP9):​c.-1342+11218C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,210 control chromosomes in the GnomAD database, including 1,344 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 0.10 (1344 hom., cov: 32)
• Consequence: NOP9 XM_005267385.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.130

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NOP9	XM_005267385.2	c.-1342+11218C>A		intron_variant			XP_005267442.1
NOP9	XM_047431052.1	c.-1660-9670C>A		intron_variant			XP_047287008.1
NOP9	XM_047431053.1	c.-1744-9670C>A		intron_variant			XP_047287009.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000288044	ENST00000669726.3	n.110+11218C>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15547 AN: 152094 Hom.: 1351 Cov.: 32

Gnomad AFR AF: 0.0799

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0798

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0722

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.102 AC: 15529 AN: 152210 Hom.: 1344 Cov.: 32 AF XY: 0.111 AC XY: 8258 AN XY: 74398

Gnomad4 AFR AF: 0.0798

Gnomad4 AMR AF: 0.0796

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.504

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.0722

Gnomad4 OTH AF: 0.0979

Alfa AF: 0.0830 Hom.: 872

Bravo AF: 0.0961

Asia WGS AF: 0.361 AC: 1256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.9
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: rs11627187; hg19: chr14-24751734;