14-24307195-C-A

Variant names:

• chr14-24307195-C-A
• rs1053649
• NM_174913.3:c.*2100C>A

Variant summary

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

The NM_174913.3(NOP9):​c.*2100C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.952 in 615,498 control chromosomes in the GnomAD database, including 279,223 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 0.94 (67887 hom., cov: 31)
  • Exomes 𝑓: 0.95 (211336 hom.)
• Consequence: NOP9 NM_174913.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220
• Publications: 6 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]

CIDEB (HGNC:1977): (cell death inducing DFFA like effector b) Enables identical protein binding activity. Involved in activation of cysteine-type endopeptidase activity; positive regulation of cell death; and positive regulation of release of cytochrome c from mitochondria. Acts upstream of or within apoptotic process. Located in cytosol and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

LTB4R2 (HGNC:19260): (leukotriene B4 receptor 2) Predicted to enable G protein-coupled peptide receptor activity and leukotriene B4 receptor activity. Predicted to be involved in inflammatory response and neuropeptide signaling pathway. Predicted to act upstream of or within keratinocyte migration and signal transduction. Located in nucleoplasm and plasma membrane. [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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NOP9	NM_174913.3	c.*2100C>A		3_prime_UTR_variant	Exon 10 of 10	ENST00000267425.8	NP_777573.1
CIDEB	NM_001393339.1	c.186+176G>T		intron_variant	Intron 2 of 4	ENST00000554411.6	NP_001380268.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NOP9	ENST00000267425.8	c.*2100C>A		3_prime_UTR_variant	Exon 10 of 10	1	NM_174913.3	ENSP00000267425.3
CIDEB	ENST00000554411.6	c.186+176G>T		intron_variant	Intron 2 of 4	1	NM_001393339.1	ENSP00000451089.1

Frequencies

GnomAD3 genomes AF: 0.944 AC: 143591 AN: 152114 Hom.: 67841 Cov.: 31

Gnomad AFR AF: 0.917

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.932

Gnomad ASJ AF: 0.963

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.948

Gnomad FIN AF: 0.975

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.964

Gnomad OTH AF: 0.946

GnomAD4 exome AF: 0.955 AC: 442285 AN: 463266 Hom.: 211336 Cov.: 6 AF XY: 0.955 AC XY: 229354 AN XY: 240204

African (AFR) AF: 0.918 AC: 11243 AN: 12252

American (AMR) AF: 0.934 AC: 13836 AN: 14806

Ashkenazi Jewish (ASJ) AF: 0.957 AC: 12045 AN: 12580

East Asian (EAS) AF: 0.851 AC: 24817 AN: 29158

South Asian (SAS) AF: 0.955 AC: 34351 AN: 35972

European-Finnish (FIN) AF: 0.975 AC: 35107 AN: 36020

Middle Eastern (MID) AF: 0.972 AC: 1835 AN: 1888

European-Non Finnish (NFE) AF: 0.965 AC: 285097 AN: 295474

Other (OTH) AF: 0.954 AC: 23954 AN: 25116

GnomAD4 genome AF: 0.944 AC: 143695 AN: 152232 Hom.: 67887 Cov.: 31 AF XY: 0.944 AC XY: 70205 AN XY: 74406

African (AFR) AF: 0.917 AC: 38061 AN: 41522

American (AMR) AF: 0.932 AC: 14257 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.963 AC: 3338 AN: 3468

East Asian (EAS) AF: 0.850 AC: 4392 AN: 5170

South Asian (SAS) AF: 0.947 AC: 4570 AN: 4824

European-Finnish (FIN) AF: 0.975 AC: 10343 AN: 10608

Middle Eastern (MID) AF: 0.963 AC: 283 AN: 294

European-Non Finnish (NFE) AF: 0.964 AC: 65554 AN: 68022

Other (OTH) AF: 0.947 AC: 2003 AN: 2116

Alfa AF: 0.958 Hom.: 108453

Bravo AF: 0.939

Asia WGS AF: 0.913 AC: 3175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.4
DANN	Benign	0.70
PhyloP100		-0.22
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1053649; hg19: chr14-24776401;