8-105601093-G-C

Position:

• chr8-105601093-G-C

Variant summary

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

The NM_012082.4(ZFPM2):​c.421-33153G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 151,928 control chromosomes in the GnomAD database, including 2,861 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 0.19 (2861 hom., cov: 32)
• Consequence: ZFPM2 NM_012082.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.572

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]

ZFPM2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZFPM2	NM_012082.4	c.421-33153G>C		intron_variant		ENST00000407775.7	NP_036214.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZFPM2	ENST00000407775.7	c.421-33153G>C		intron_variant		1	NM_012082.4	ENSP00000384179.2

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28653 AN: 151810 Hom.: 2854 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.112

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.189 AC: 28677 AN: 151928 Hom.: 2861 Cov.: 32 AF XY: 0.193 AC XY: 14320 AN XY: 74228

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.169

Alfa AF: 0.108 Hom.: 179

Bravo AF: 0.180

Asia WGS AF: 0.198 AC: 689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.39

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: rs17217757; hg19: chr8-106613321;