20-32498054-A-G

Variant names:

• chr20-32498054-A-G
• rs293554
• NM_001256798.2:c.699+13293T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

Genes affected

NOL4L (HGNC:16106): (nucleolar protein 4 like) Located in cytosol and nucleoplasm. [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=-0.76).
• 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 rank	MANE	Protein	UniProt
NOL4L	NM_001256798.2	c.699+13293T>C		intron_variant	Intron 4 of 10	ENST00000621426.7	NP_001243727.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NOL4L	ENST00000621426.7	c.699+13293T>C		intron_variant	Intron 4 of 10	5	NM_001256798.2	ENSP00000483523.1
NOL4L	ENST00000201961.6	c.637-11253T>C		intron_variant	Intron 4 of 5	3		ENSP00000201961.3
NOL4L	ENST00000375678.7	c.294+13293T>C		intron_variant	Intron 6 of 7	2		ENSP00000364830.3
NOL4L	ENST00000375677.5	c.60+13293T>C		intron_variant	Intron 1 of 2	3		ENSP00000364829.2

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

African (AFR) AF: 0.732 AC: 30372 AN: 41502

American (AMR) AF: 0.573 AC: 8758 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1028 AN: 3466

East Asian (EAS) AF: 0.988 AC: 5111 AN: 5172

South Asian (SAS) AF: 0.490 AC: 2364 AN: 4822

European-Finnish (FIN) AF: 0.550 AC: 5821 AN: 10582

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.396 AC: 26938 AN: 67968

Other (OTH) AF: 0.507 AC: 1068 AN: 2108

Alfa AF: 0.440 Hom.: 45380

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
PhyloP100		0.011
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs293554; hg19: chr20-31085857;