ZNF566 p.His146His

Variant names:

• chr19-36449795-C-C
• NM_001145344.1:c.

Your query was ambiguous. Multiple possible variants found:

• chr19-36449796--
• chr19-36449796-A-G

Variant summary

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

The NM_001145344.1(ZNF566):​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: 32)
• Consequence: ZNF566 NM_001145344.1 exon_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300
• Publications: 0 publications found

Genes affected

ZNF566 (HGNC:25919): (zinc finger protein 566) Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. Predicted to be integral component of membrane. [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_001145344.1. 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
	ZNF566	NM_001145344.1	MANE Select	c.		exon_region	Exon 5 of 5	NP_001138816.1	Q969W8-1
	ZNF566	NM_001145343.1		c.		exon_region	Exon 5 of 5	NP_001138815.1	Q969W8-2
	ZNF566	NM_001437584.1		c.		exon_region	Exon 5 of 5	NP_001424513.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF566	ENST00000452939.7	TSL:2 MANE Select	c.		exon_region	Exon 5 of 5	ENSP00000411526.2	Q969W8-1
	ZNF566	ENST00000493391.6	TSL:1	c.		exon_region	Exon 3 of 3	ENSP00000465343.1	B4DRR6
	ZNF566	ENST00000392170.7	TSL:5	c.		exon_region	Exon 5 of 5	ENSP00000376010.2	Q969W8-2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.0030

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: chr19-36940697;