rs16873291

chr8-105515802-C-T

Variant summary

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

The NM_012082.4(ZFPM2):c.302-45561C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 151,730 control chromosomes in the GnomAD database, including 14,766 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 0.40 (14766 hom., cov: 31)
• Consequence: ZFPM2 NM_012082.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZFPM2	NM_012082.4	c.302-45561C>T		intron_variant		ENST00000407775.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZFPM2	ENST00000407775.7	c.302-45561C>T		intron_variant		1	NM_012082.4	P1

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60231 AN: 151616 Hom.: 14744 Cov.: 31

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.397 AC: 60296 AN: 151730 Hom.: 14766 Cov.: 31 AF XY: 0.392 AC XY: 29045 AN XY: 74094

Gnomad4 AFR AF: 0.701

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.289

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.385

Alfa AF: 0.346 Hom.: 1819

Bravo AF: 0.414

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.12
Dann	Benign	0.30

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs16873291; hg19: chr8-106528030;