rs3940231

Variant names:

• chr14-24279157-C-T
• rs3940231
• XM_005267385.2:c.-1342+7847C>T

Variant summary

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

The ENST00000669726.4(ENSG00000288044):​n.120+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: ENSG00000288044 ENST00000669726.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220
• Publications: 12 publications found

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

Our verdict: Benign. The variant received -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.

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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288044	ENST00000669726.4		n.120+7847C>T		intron	N/A
	ENSG00000288044	ENST00000716589.1		n.104+7847C>T		intron	N/A
	ENSG00000288044	ENST00000716590.1		n.114+1781C>T		intron	N/A

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

African (AFR) AF: 0.722 AC: 29943 AN: 41470

American (AMR) AF: 0.517 AC: 7903 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1541 AN: 3472

East Asian (EAS) AF: 0.594 AC: 3069 AN: 5170

South Asian (SAS) AF: 0.585 AC: 2815 AN: 4814

European-Finnish (FIN) AF: 0.362 AC: 3817 AN: 10530

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

European-Non Finnish (NFE) AF: 0.373 AC: 25302 AN: 67914

Other (OTH) AF: 0.476 AC: 1003 AN: 2108

Alfa AF: 0.413 Hom.: 9146

Bravo AF: 0.520

Asia WGS AF: 0.607 AC: 2111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.1
DANN	Benign	0.28
PhyloP100		0.022

Splicing

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

Other links and lift over

dbSNP: rs3940231; hg19: chr14-24748363;