rs371649171

Variant names:

• chr20-32452340-G-A
• rs371649171
• NM_001256798.2:c.1718C>T

Your query was ambiguous. Multiple possible variants found:

• chr20-32452340-G-A
• chr20-32452340-G-C

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001256798.2(NOL4L):​c.1718C>T​(p.Pro573Leu) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P573R) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: NOL4L NM_001256798.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.85
• Publications: 0 publications found

Genes affected

NOL4L (HGNC:16106): (nucleolar protein 4 like) Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000236772 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NOL4L	NM_001256798.2	c.1718C>T	p.Pro573Leu	missense_variant	Exon 10 of 11	ENST00000621426.7	NP_001243727.1
NOL4L	NM_080616.6	c.986C>T	p.Pro329Leu	missense_variant	Exon 7 of 8		NP_542183.2
NOL4L	NM_001351680.2	c.986C>T	p.Pro329Leu	missense_variant	Exon 7 of 9		NP_001338609.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NOL4L	ENST00000621426.7	c.1718C>T	p.Pro573Leu	missense_variant	Exon 10 of 11	5	NM_001256798.2	ENSP00000483523.1
ENSG00000236772	ENST00000442179.1	n.716+627G>A		intron_variant	Intron 3 of 3	1
NOL4L	ENST00000359676.9	c.986C>T	p.Pro329Leu	missense_variant	Exon 7 of 8	2		ENSP00000352704.5

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Uncertain	0.014	T
BayesDel_noAF	Benign	-0.22
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Benign	0.27	T;T;.
Eigen	Uncertain	0.33
Eigen_PC	Uncertain	0.39
FATHMM_MKL	Uncertain	0.92	D
LIST_S2	Uncertain	0.96	D;D;D
M_CAP	Benign	0.0084	T
MetaRNN	Uncertain	0.51	D;D;D
MetaSVM	Benign	-0.85	T
PhyloP100		6.8
PROVEAN	Uncertain	-3.2	D;.;.
REVEL	Benign	0.11
Sift	Benign	0.27	T;.;.
Sift4G	Benign	0.35	T;T;T
Polyphen		0.78	P;.;.
Vest4		0.78
MutPred		0.38		Loss of loop (P = 0.0203);.;Loss of loop (P = 0.0203);
MVP		0.082
MPC		0.55
ClinPred		0.96	D
GERP RS		4.7
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.096
gMVP		0.32
Mutation Taster		=67/33	polymorphism

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

Other links and lift over

dbSNP: rs371649171; hg19: chr20-31040143; COSMIC: COSV62890143; COSMIC: COSV62890143;