rs1521774

Positions:

• chr8-104966762-G-A

Variant summary

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

The ENST00000518180.1(ZFPM2):​n.197-24862G>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 0.553 in 152,026 control chromosomes in the GnomAD database, including 24,877 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 0.55 (24877 hom., cov: 32)
• Consequence: ZFPM2 ENST00000518180.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184

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 (SAS) allele frequency at 95% confidence interval = 0.706 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.197-24862G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.553 AC: 84078 AN: 151908 Hom.: 24877 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.553 AC: 84090 AN: 152026 Hom.: 24877 Cov.: 32 AF XY: 0.548 AC XY: 40740 AN XY: 74312

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.597

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.579

Gnomad4 SAS AF: 0.727

Gnomad4 FIN AF: 0.462

Gnomad4 NFE AF: 0.664

Gnomad4 OTH AF: 0.592

Alfa AF: 0.642 Hom.: 14479

Bravo AF: 0.554

Asia WGS AF: 0.593 AC: 2062 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.94
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: rs1521774; hg19: chr8-105978990;