ZNF488 p.Gly21Gly

Variant names:

• chr10-47368766-T-T
• NM_153034.4:c.

Your query was ambiguous. Multiple possible variants found:

• chr10-47368767--
• chr10-47368767-C-A
• chr10-47368767-C-G
• chr10-47368767-C-T

Variant summary

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

The NM_153034.4(ZNF488):​c. variant causes a exon region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: ZNF488 NM_153034.4 exon_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349
• Publications: 0 publications found

Genes affected

ZNF488 (HGNC:23535): (zinc finger protein 488) Predicted to enable DNA binding activity and metal ion binding activity. Predicted to be involved in oligodendrocyte development; positive regulation of myelination; and regulation of transcription, DNA-templated. Predicted to act upstream of or within negative regulation of transcription, DNA-templated and positive regulation of oligodendrocyte differentiation. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153034.4. 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
	ZNF488	NM_153034.4	MANE Select	c.		exon_region	Exon 2 of 2	NP_694579.1	Q96MN9-1
	ZNF488	NM_001346932.2		c.		exon_region	Exon 4 of 4	NP_001333861.1	Q96MN9-1
	ZNF488	NM_001346933.2		c.		exon_region	Exon 3 of 3	NP_001333862.1	Q96MN9-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF488	ENST00000585316.3	TSL:1 MANE Select	c.		exon_region	Exon 2 of 2	ENSP00000462269.1	Q96MN9-1
	ZNF488	ENST00000591025.1	TSL:1	c.		exon_region	Exon 2 of 3	ENSP00000468133.1	Q96MN9-2
	ZNF488	ENST00000591025.1	TSL:1	c.		5_prime_UTR	Exon 2 of 3	ENSP00000468133.1	Q96MN9-2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 47

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.35

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr10-48370596;