8-28527193-TTA-CTC

Variant names:

• chr8-28527193-TTA-CTC
• NM_017412.4:c.433_435delTTAinsCTC
• FZD3 p.146

Variant summary

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

The NM_017412.4(FZD3):​c.433_435delTTAinsCTC​(p.146) variant causes a synonymous change. 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.

• Frequency: Genomes: not found (cov: 30)
• Consequence: FZD3 NM_017412.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.62
• Publications: 0 publications found

Genes affected

FZD3 (HGNC:4041): (frizzled class receptor 3) This gene is a member of the frizzled gene family. Members of this family encode seven-transmembrane domain proteins that are receptors for the wingless type MMTV integration site family of signaling proteins. Most frizzled receptors are coupled to the beta-catenin canonical signaling pathway. The function of this protein is unknown, although it may play a role in mammalian hair follicle development. Alternative splicing results in multiple transcript variants. This gene is a susceptibility locus for schizophrenia. [provided by RefSeq, Dec 2010]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017412.4. 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
	FZD3	NM_017412.4	MANE Select	c.433_435delTTAinsCTC	p.146	synonymous	N/A	NP_059108.1	Q9NPG1-1
	FZD3	NM_001412905.1		c.502_504delTTAinsCTC	p.169	synonymous	N/A	NP_001399834.1
	FZD3	NM_001412917.1		c.502_504delTTAinsCTC	p.169	synonymous	N/A	NP_001399846.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FZD3	ENST00000240093.8	TSL:1 MANE Select	c.433_435delTTAinsCTC	p.146	synonymous	N/A	ENSP00000240093.3	Q9NPG1-1
	FZD3	ENST00000927846.1		c.502_504delTTAinsCTC	p.169	synonymous	N/A	ENSP00000597905.1
	FZD3	ENST00000537916.2	TSL:2	c.433_435delTTAinsCTC	p.146	synonymous	N/A	ENSP00000437489.1	Q9NPG1-1

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
PhyloP100		3.6

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: chr8-28384710;