rs285814

chr8-105096256-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000518180.1(ZFPM2):n.242+104587T>C 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 0.336 in 152,008 control chromosomes in the GnomAD database, including 9,898 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 0.34 (9898 hom., cov: 32)
• Consequence: ZFPM2 ENST00000518180.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.20

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.424 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+104587T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51121 AN: 151888 Hom.: 9903 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.336 AC: 51124 AN: 152008 Hom.: 9898 Cov.: 32 AF XY: 0.335 AC XY: 24916 AN XY: 74294

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.415

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.428

Gnomad4 OTH AF: 0.350

Alfa AF: 0.374 Hom.: 1436

Bravo AF: 0.335

Asia WGS AF: 0.269 AC: 937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
Cadd	Benign	22
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs285814; hg19: chr8-106108484;