8-105801244-AGC-TCT

Variant names:

• chr8-105801244-AGC-TCT
• NM_012082.4:c.1162_1164delAGCinsTCT
• ZFPM2 p.389

Variant summary

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

The NM_012082.4(ZFPM2):​c.1162_1164delAGCinsTCT​(p.389) 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. Synonymous variant affecting the same amino acid position (i.e. S388S) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ZFPM2 NM_012082.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.43
• Publications: 0 publications found

Genes affected

ZFPM2 (HGNC:16700): (zinc finger protein, FOG family member 2) The zinc finger protein encoded by this gene is a widely expressed member of the FOG family of transcription factors. The family members modulate the activity of GATA family proteins, which are important regulators of hematopoiesis and cardiogenesis in mammals. It has been demonstrated that the protein can both activate and down-regulate expression of GATA-target genes, suggesting different modulation in different promoter contexts. A related mRNA suggests an alternatively spliced product but this information is not yet fully supported by the sequence. [provided by RefSeq, Jul 2008]

ZFPM2-AS1 (HGNC:50698): (ZFPM2 antisense RNA 1)

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012082.4. 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
	ZFPM2	NM_012082.4	MANE Select	c.1162_1164delAGCinsTCT	p.389	synonymous	N/A	NP_036214.2	Q8WW38-1
	ZFPM2	NM_001362836.2		c.1003_1005delAGCinsTCT	p.336	synonymous	N/A	NP_001349765.1
	ZFPM2	NM_001362837.2		c.766_768delAGCinsTCT	p.257	synonymous	N/A	NP_001349766.1	E7ET52

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFPM2	ENST00000407775.7	TSL:1 MANE Select	c.1162_1164delAGCinsTCT	p.389	synonymous	N/A	ENSP00000384179.2	Q8WW38-1
	ZFPM2	ENST00000941376.1		c.1159_1161delAGCinsTCT	p.388	synonymous	N/A	ENSP00000611435.1
	ZFPM2	ENST00000517361.1	TSL:2	c.766_768delAGCinsTCT	p.257	synonymous	N/A	ENSP00000428720.1	E7ET52

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		6.4

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: chr8-106813472;