rs977396

Positions:

• chr8-104980468-G-A

Variant summary

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

The ENST00000518180.1(ZFPM2):​n.197-11156G>A 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 0.897 in 152,128 control chromosomes in the GnomAD database, including 61,424 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 0.90 (61424 hom., cov: 32)
• Consequence: ZFPM2 ENST00000518180.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.709

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.963 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.197-11156G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.897 AC: 136324 AN: 152010 Hom.: 61367 Cov.: 32

Gnomad AFR AF: 0.970

Gnomad AMI AF: 0.954

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.933

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.879

Gnomad OTH AF: 0.879

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

GnomAD4 genome AF: 0.897 AC: 136438 AN: 152128 Hom.: 61424 Cov.: 32 AF XY: 0.893 AC XY: 66405 AN XY: 74348

Gnomad4 AFR AF: 0.971

Gnomad4 AMR AF: 0.853

Gnomad4 ASJ AF: 0.882

Gnomad4 EAS AF: 0.835

Gnomad4 SAS AF: 0.933

Gnomad4 FIN AF: 0.803

Gnomad4 NFE AF: 0.879

Gnomad4 OTH AF: 0.877

Alfa AF: 0.882 Hom.: 128176

Bravo AF: 0.904

Asia WGS AF: 0.871 AC: 3027 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.44
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs977396; hg19: chr8-105992696;