rs71305152

Positions:

• chr8-105437494-A-ATTTTCT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_012082.4(ZFPM2):​c.200-6785_200-6780dup variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.42 (14872 hom., cov: 0)
• Consequence: ZFPM2 NM_012082.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.104

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]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZFPM2	NM_012082.4	c.200-6785_200-6780dup		intron_variant		ENST00000407775.7	NP_036214.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZFPM2	ENST00000407775.7	c.200-6785_200-6780dup		intron_variant		1	NM_012082.4	ENSP00000384179	P1

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64275 AN: 151348 Hom.: 14844 Cov.: 0

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.425 AC: 64369 AN: 151466 Hom.: 14872 Cov.: 0 AF XY: 0.428 AC XY: 31637 AN XY: 74000

Gnomad4 AFR AF: 0.622

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.419

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.377

Alfa AF: 0.386 Hom.: 1240

Asia WGS AF: 0.407 AC: 1418 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs71305152; hg19: chr8-106449722;