8-105130105-C-T

Position:

• chr8-105130105-C-T

Variant summary

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

The ENST00000518180.1(ZFPM2):​n.243-116188C>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 0.735 in 152,134 control chromosomes in the GnomAD database, including 41,130 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 0.73 (41130 hom., cov: 33)
• Consequence: ZFPM2 ENST00000518180.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.751 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZFPM2	ENST00000518180.1	n.243-116188C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.735 AC: 111691 AN: 152016 Hom.: 41104 Cov.: 33

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.794

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.735 AC: 111774 AN: 152134 Hom.: 41130 Cov.: 33 AF XY: 0.735 AC XY: 54690 AN XY: 74380

Gnomad4 AFR AF: 0.753

Gnomad4 AMR AF: 0.679

Gnomad4 ASJ AF: 0.788

Gnomad4 EAS AF: 0.771

Gnomad4 SAS AF: 0.725

Gnomad4 FIN AF: 0.771

Gnomad4 NFE AF: 0.724

Gnomad4 OTH AF: 0.746

Alfa AF: 0.727 Hom.: 48031

Bravo AF: 0.726

Asia WGS AF: 0.772 AC: 2683 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.46
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9297357; hg19: chr8-106142333;