8-105318866-G-GGCGGCGGGAGCGGCGGGAGCCGCGGGA

Variant names:

• chr8-105318866-G-GGCGGCGGGAGCGGCGGGAGCCGCGGGA
• rs71305140
• NM_012082.4:c.-65_-64insGGCGGGAGCCGCGGGAGCGGCGGGAGC

Variant summary

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

The NM_012082.4(ZFPM2):​c.-65_-64insGGCGGGAGCCGCGGGAGCGGCGGGAGC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, 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: 0)
• Consequence: ZFPM2 NM_012082.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.37
• Publications: 1 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 Gene-Disease associations (from GenCC):

• 46,XY sex reversal 9

  Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• diaphragmatic hernia 3

  Inheritance: AD Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), G2P
• tetralogy of fallot

  Inheritance: Unknown, AD Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
• 46,XY partial gonadal dysgenesis

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZFPM2	NM_012082.4	c.-65_-64insGGCGGGAGCCGCGGGAGCGGCGGGAGC		5_prime_UTR_variant	Exon 1 of 8	ENST00000407775.7	NP_036214.2
ZFPM2	NM_001362836.2	c.-65_-64insGGCGGGAGCCGCGGGAGCGGCGGGAGC		5_prime_UTR_variant	Exon 1 of 7		NP_001349765.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZFPM2	ENST00000407775.7	c.-65_-64insGGCGGGAGCCGCGGGAGCGGCGGGAGC		5_prime_UTR_variant	Exon 1 of 8	1	NM_012082.4	ENSP00000384179.2
ZFPM2	ENST00000518180.1	n.479+72348_479+72349insGGCGGGAGCCGCGGGAGCGGCGGGAGC		intron_variant	Intron 4 of 4	4

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Cov.: 13

GnomAD4 genome Cov.: 0

Alfa AF: 0.00 Hom.: 1334

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.4

Splicing

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

Other links and lift over

dbSNP: rs71305140; hg19: chr8-106331094;