rs293553

Variant names:

• chr20-32497557-A-C
• rs293553
• NM_001256798.2:c.699+13790T>G

Your query was ambiguous. Multiple possible variants found:

• chr20-32497557-A-C
• chr20-32497557-A-G
• chr20-32497557-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001256798.2(NOL4L):​c.699+13790T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
• Consequence: NOL4L NM_001256798.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 1 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001256798.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NOL4L	NM_001256798.2	MANE Select	c.699+13790T>G		intron	N/A	NP_001243727.1	A0A087X0N3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NOL4L	ENST00000621426.7	TSL:5 MANE Select	c.699+13790T>G		intron	N/A	ENSP00000483523.1	A0A087X0N3
	NOL4L	ENST00000201961.6	TSL:3	c.637-10756T>G		intron	N/A	ENSP00000201961.3	Q5W149
	NOL4L	ENST00000375678.7	TSL:2	c.294+13790T>G		intron	N/A	ENSP00000364830.3	Q5JYC0

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.039
DANN	Benign	0.34
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs293553; hg19: chr20-31085360;