rs725403

Positions:

• chr8-104697008-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000521923.5(ZFPM2):​n.37-17838A>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.618 in 151,998 control chromosomes in the GnomAD database, including 29,956 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.62 (29956 hom., cov: 32)
• Consequence: ZFPM2 ENST00000521923.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.32

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZFPM2	ENST00000521923.5	n.37-17838A>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.618 AC: 93838 AN: 151878 Hom.: 29928 Cov.: 32

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.618 AC: 93909 AN: 151998 Hom.: 29956 Cov.: 32 AF XY: 0.616 AC XY: 45795 AN XY: 74304

Gnomad4 AFR AF: 0.479

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.505

Gnomad4 SAS AF: 0.606

Gnomad4 FIN AF: 0.737

Gnomad4 NFE AF: 0.713

Gnomad4 OTH AF: 0.571

Alfa AF: 0.671 Hom.: 4330

Bravo AF: 0.591

Asia WGS AF: 0.561 AC: 1953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.6
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs725403; hg19: chr8-105709236;