rs1452643

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
NOL4	NM_003787.5	c.1543-24040A>T		intron_variant		ENST00000261592.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NOL4	ENST00000261592.10	c.1543-24040A>T		intron_variant		1	NM_003787.5	P1

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

Gnomad4 AFR AF: 0.887

Gnomad4 AMR AF: 0.880

Gnomad4 ASJ AF: 0.834

Gnomad4 EAS AF: 0.965

Gnomad4 SAS AF: 0.783

Gnomad4 FIN AF: 0.867

Gnomad4 NFE AF: 0.817

Gnomad4 OTH AF: 0.852

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs1452643; hg19: chr18-31487428;