20-32497557-A-G

Position:

• chr20-32497557-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+13790T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.533 in 151,974 control chromosomes in the GnomAD database, including 23,740 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 0.53 (23740 hom., cov: 30)
• Consequence: NOL4L NM_001256798.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86

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=-0.92).
• 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	Protein	UniProt
NOL4L	NM_001256798.2	c.699+13790T>C		intron_variant		ENST00000621426.7	NP_001243727.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NOL4L	ENST00000621426.7	c.699+13790T>C		intron_variant		5	NM_001256798.2	ENSP00000483523.1
NOL4L	ENST00000201961.6	c.637-10756T>C		intron_variant		3		ENSP00000201961.3
NOL4L	ENST00000375678.7	c.294+13790T>C		intron_variant		2		ENSP00000364830.3
NOL4L	ENST00000375677.5	c.60+13790T>C		intron_variant		3		ENSP00000364829.2

Frequencies

GnomAD3 genomes AF: 0.533 AC: 80970 AN: 151856 Hom.: 23694 Cov.: 30

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.533 AC: 81078 AN: 151974 Hom.: 23740 Cov.: 30 AF XY: 0.543 AC XY: 40311 AN XY: 74292

Gnomad4 AFR AF: 0.714

Gnomad4 AMR AF: 0.572

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.988

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.550

Gnomad4 NFE AF: 0.396

Gnomad4 OTH AF: 0.502

Alfa AF: 0.476 Hom.: 2301

Bravo AF: 0.548

Asia WGS AF: 0.738 AC: 2562 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.044
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs293553; hg19: chr20-31085360;