rs7845583

chr8-104698507-G-Achr8-104698507-G-T

Variant summary

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

The ENST00000521923.5(ZFPM2):n.37-16339G>A 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 0.662 in 151,958 control chromosomes in the GnomAD database, including 33,726 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 0.66 (33726 hom., cov: 32)
• Consequence: ZFPM2 ENST00000521923.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.302

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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.709 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.37-16339G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100550 AN: 151840 Hom.: 33692 Cov.: 32

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.739

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.662 AC: 100633 AN: 151958 Hom.: 33726 Cov.: 32 AF XY: 0.659 AC XY: 48962 AN XY: 74250

Gnomad4 AFR AF: 0.631

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.506

Gnomad4 SAS AF: 0.608

Gnomad4 FIN AF: 0.739

Gnomad4 NFE AF: 0.714

Gnomad4 OTH AF: 0.609

Alfa AF: 0.673 Hom.: 5134

Bravo AF: 0.641

Asia WGS AF: 0.568 AC: 1975 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.0
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7845583; hg19: chr8-105710735;