rs284495

Positions:

• chr8-104953350-T-C
• chr8-104953350-T-G

Variant summary

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

The ENST00000518180.1(ZFPM2):​n.197-38274T>C 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 0.439 in 151,890 control chromosomes in the GnomAD database, including 16,001 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 0.44 (16001 hom., cov: 33)
• Consequence: ZFPM2 ENST00000518180.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210

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 = 0.621 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.197-38274T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66602 AN: 151772 Hom.: 15956 Cov.: 33

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.439 AC: 66704 AN: 151890 Hom.: 16001 Cov.: 33 AF XY: 0.444 AC XY: 32973 AN XY: 74208

Gnomad4 AFR AF: 0.627

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.336

Gnomad4 OTH AF: 0.401

Alfa AF: 0.363 Hom.: 5635

Bravo AF: 0.437

Asia WGS AF: 0.407 AC: 1416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.72
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs284495; hg19: chr8-105965578;