rs285778

chr8-105099728-C-T

Variant summary

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

The ENST00000518180.1(ZFPM2):n.242+108059C>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 0.842 in 152,172 control chromosomes in the GnomAD database, including 54,347 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 0.84 (54347 hom., cov: 32)
• Consequence: ZFPM2 ENST00000518180.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.325

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 (EAS) allele frequency at 95% confidence interval = 0.976 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	ENST00000518180.1	n.242+108059C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.842 AC: 128000 AN: 152054 Hom.: 54317 Cov.: 32

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.977

Gnomad AMR AF: 0.885

Gnomad ASJ AF: 0.877

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.938

Gnomad FIN AF: 0.909

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.859

Gnomad OTH AF: 0.860

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

GnomAD4 genome AF: 0.842 AC: 128084 AN: 152172 Hom.: 54347 Cov.: 32 AF XY: 0.847 AC XY: 62976 AN XY: 74388

Gnomad4 AFR AF: 0.742

Gnomad4 AMR AF: 0.885

Gnomad4 ASJ AF: 0.877

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.938

Gnomad4 FIN AF: 0.909

Gnomad4 NFE AF: 0.859

Gnomad4 OTH AF: 0.861

Alfa AF: 0.846 Hom.: 11484

Bravo AF: 0.837

Asia WGS AF: 0.950 AC: 3305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.82
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs285778; hg19: chr8-106111956;