14-24282528-C-A

Variant names:

• chr14-24282528-C-A
• rs11627187
• ENST00000669726.4:n.120+11218C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000669726.4(ENSG00000288044):​n.120+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: ENSG00000288044 ENST00000669726.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.130
• Publications: 7 publications found

Genes affected

ENSG00000288044 (HGNC:):

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000669726.4. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288044	ENST00000669726.4		n.120+11218C>A		intron	N/A
	ENSG00000288044	ENST00000716589.1		n.105-9181C>A		intron	N/A
	ENSG00000288044	ENST00000716590.1		n.114+5152C>A		intron	N/A

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

African (AFR) AF: 0.0798 AC: 3313 AN: 41532

American (AMR) AF: 0.0796 AC: 1217 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 457 AN: 3468

East Asian (EAS) AF: 0.504 AC: 2600 AN: 5156

South Asian (SAS) AF: 0.267 AC: 1288 AN: 4822

European-Finnish (FIN) AF: 0.139 AC: 1474 AN: 10598

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0722 AC: 4913 AN: 68016

Other (OTH) AF: 0.0979 AC: 207 AN: 2114

Alfa AF: 0.0824 Hom.: 1083

Bravo AF: 0.0961

Asia WGS AF: 0.361 AC: 1256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.9
DANN	Benign	0.52
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs11627187; hg19: chr14-24751734;