rs285866

chr8-105051229-A-G

Variant summary

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

The ENST00000518180.1(ZFPM2):n.242+59560A>G 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 0.33 in 152,094 control chromosomes in the GnomAD database, including 9,979 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 0.33 (9979 hom., cov: 33)
• Consequence: ZFPM2 ENST00000518180.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.887

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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.427 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+59560A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50118 AN: 151976 Hom.: 9984 Cov.: 33

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.330 AC: 50115 AN: 152094 Hom.: 9979 Cov.: 33 AF XY: 0.331 AC XY: 24607 AN XY: 74322

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.442

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.353

Alfa AF: 0.379 Hom.: 2033

Bravo AF: 0.325

Asia WGS AF: 0.283 AC: 979 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.63
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs285866; hg19: chr8-106063457;