rs1452643

Variant names:

• chr18-33907464-T-A
• rs1452643
• NM_003787.5:c.1543-24040A>T

Your query was ambiguous. Multiple possible variants found:

• chr18-33907464-T-A
• chr18-33907464-T-C
• chr18-33907464-T-G

Variant summary

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

The NM_003787.5(NOL4):​c.1543-24040A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.851 in 152,094 control chromosomes in the GnomAD database, including 55,154 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 0.85 (55154 hom., cov: 31)
• Consequence: NOL4 NM_003787.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.587
• Publications: 1 publications found

Genes affected

NOL4 (HGNC:7870): (nucleolar protein 4) Predicted to enable RNA binding activity. Predicted to be located 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.943 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NOL4	NM_003787.5	c.1543-24040A>T		intron_variant	Intron 9 of 10	ENST00000261592.10	NP_003778.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NOL4	ENST00000261592.10	c.1543-24040A>T		intron_variant	Intron 9 of 10	1	NM_003787.5	ENSP00000261592.4

Frequencies

GnomAD3 genomes AF: 0.851 AC: 129284 AN: 151976 Hom.: 55086 Cov.: 31

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.880

Gnomad ASJ AF: 0.834

Gnomad EAS AF: 0.965

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.867

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.817

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.851 AC: 129411 AN: 152094 Hom.: 55154 Cov.: 31 AF XY: 0.854 AC XY: 63467 AN XY: 74350

African (AFR) AF: 0.887 AC: 36782 AN: 41488

American (AMR) AF: 0.880 AC: 13438 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.834 AC: 2894 AN: 3470

East Asian (EAS) AF: 0.965 AC: 5007 AN: 5186

South Asian (SAS) AF: 0.783 AC: 3773 AN: 4816

European-Finnish (FIN) AF: 0.867 AC: 9155 AN: 10558

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.817 AC: 55558 AN: 67984

Other (OTH) AF: 0.852 AC: 1803 AN: 2116

Alfa AF: 0.833 Hom.: 6557

Bravo AF: 0.858

Asia WGS AF: 0.900 AC: 3128 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.1
DANN	Benign	0.41
PhyloP100		0.59
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: rs1452643; hg19: chr18-31487428;