20-32498054-A-G

Variant summary

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

The NM_001256798.2(NOL4L):c.699+13293T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 152,110 control chromosomes in the GnomAD database, including 24,301 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 0.54 (24301 hom., cov: 32)
• Consequence: NOL4L NM_001256798.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110

Genes affected

NOL4L (HGNC:16106): (nucleolar protein 4 like) Located in cytosol and nucleoplasm. [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=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.966 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NOL4L	NM_001256798.2	c.699+13293T>C		intron_variant		ENST00000621426.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NOL4L	ENST00000621426.7	c.699+13293T>C		intron_variant		5	NM_001256798.2	P1
NOL4L	ENST00000201961.6	c.638-11253T>C		intron_variant		3
NOL4L	ENST00000375677.5	c.61+13293T>C		intron_variant		3
NOL4L	ENST00000375678.7	c.294+13293T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81816 AN: 151992 Hom.: 24255 Cov.: 32

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.539 AC: 81924 AN: 152110 Hom.: 24301 Cov.: 32 AF XY: 0.547 AC XY: 40705 AN XY: 74374

Gnomad4 AFR AF: 0.732

Gnomad4 AMR AF: 0.573

Gnomad4 ASJ AF: 0.297

Gnomad4 EAS AF: 0.988

Gnomad4 SAS AF: 0.490

Gnomad4 FIN AF: 0.550

Gnomad4 NFE AF: 0.396

Gnomad4 OTH AF: 0.507

Alfa AF: 0.409 Hom.: 25714

Bravo AF: 0.555

Asia WGS AF: 0.740 AC: 2569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	11
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs293554; hg19: chr20-31085857;