rs1460239

Positions:

• chr8-104799137-C-T

Variant summary

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

The ENST00000518180.1(ZFPM2):​n.196+84162C>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 0.486 in 151,984 control chromosomes in the GnomAD database, including 18,899 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 0.49 (18899 hom., cov: 33)
• Consequence: ZFPM2 ENST00000518180.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.224

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=-0.3).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.566 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.196+84162C>T		intron_variant, non_coding_transcript_variant		4
ZFPM2	ENST00000521923.5	n.167-28220C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73768 AN: 151866 Hom.: 18897 Cov.: 33

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.486 AC: 73794 AN: 151984 Hom.: 18899 Cov.: 33 AF XY: 0.483 AC XY: 35835 AN XY: 74268

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.571

Gnomad4 FIN AF: 0.486

Gnomad4 NFE AF: 0.571

Gnomad4 OTH AF: 0.507

Alfa AF: 0.545 Hom.: 11408

Bravo AF: 0.481

Asia WGS AF: 0.389 AC: 1354 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	18
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1460239; hg19: chr8-105811365;