chr19-15423130-TGG-ACT

Variant names:

• chr19-15423130-TGG-ACT
• NM_001371589.1:c.5614_5616delCCAinsAGT
• WIZ p.Pro1872Ser

Variant summary

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

The NM_001371589.1(WIZ):​c.5614_5616delCCAinsAGT​(p.Pro1872Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P1872A) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: WIZ NM_001371589.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.84
• Publications: 0 publications found

Genes affected

WIZ (HGNC:30917): (WIZ zinc finger) Enables several functions, including DNA-binding transcription factor activity, RNA polymerase II-specific; histone methyltransferase binding activity; and transcription corepressor binding activity. Involved in positive regulation of nuclear cell cycle DNA replication and protein stabilization. Located in midbody and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001371589.1. 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
	WIZ	NM_001371589.1	MANE Select	c.5614_5616delCCAinsAGT	p.Pro1872Ser	missense	N/A	NP_001358518.1	A0A669KAV7
	WIZ	NM_001439242.1		c.5215_5217delCCAinsAGT	p.Pro1739Ser	missense	N/A	NP_001426171.1
	WIZ	NM_001411129.1		c.5044_5046delCCAinsAGT	p.Pro1682Ser	missense	N/A	NP_001398058.1	A0A2R8YFV2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WIZ	ENST00000673675.1	MANE Select	c.5614_5616delCCAinsAGT	p.Pro1872Ser	missense	N/A	ENSP00000500993.1	A0A669KAV7
	WIZ	ENST00000545156.5	TSL:1	c.2842_2844delCCAinsAGT	p.Pro948Ser	missense	N/A	ENSP00000445824.1	O95785-3
	WIZ	ENST00000389282.8	TSL:1	c.2443_2445delCCAinsAGT	p.Pro815Ser	missense	N/A	ENSP00000373933.5	B9EGQ5

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.8

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: chr19-15533941;