rs12185438

chr18-34091638-G-Achr18-34091638-G-Cchr18-34091638-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003787.5(NOL4):c.772+1827C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 151,902 control chromosomes in the GnomAD database, including 17,991 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 0.48 (17991 hom., cov: 31)
• Consequence: NOL4 NM_003787.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.820

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NOL4	NM_003787.5	c.772+1827C>T		intron_variant		ENST00000261592.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NOL4	ENST00000261592.10	c.772+1827C>T		intron_variant		1	NM_003787.5	P1

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73306 AN: 151784 Hom.: 17945 Cov.: 31

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.483 AC: 73414 AN: 151902 Hom.: 17991 Cov.: 31 AF XY: 0.485 AC XY: 36014 AN XY: 74242

Gnomad4 AFR AF: 0.522

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.505

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.508

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.474

Alfa AF: 0.453 Hom.: 29148

Bravo AF: 0.489

Asia WGS AF: 0.457 AC: 1586 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.5
Dann	Benign	0.54

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: rs12185438; hg19: chr18-31671602;