rs1901062

Positions:

• chr8-105577306-G-A
• chr8-105577306-G-C
• chr8-105577306-G-T

Variant summary

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

The NM_012082.4(ZFPM2):​c.420+15825G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 151,904 control chromosomes in the GnomAD database, including 33,147 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 0.65 (33147 hom., cov: 32)
• Consequence: ZFPM2 NM_012082.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140

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-AS1 (HGNC:50698): (ZFPM2 antisense RNA 1)

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 = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZFPM2	NM_012082.4	c.420+15825G>A		intron_variant		ENST00000407775.7	NP_036214.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZFPM2	ENST00000407775.7	c.420+15825G>A		intron_variant		1	NM_012082.4	ENSP00000384179	P1

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99228 AN: 151786 Hom.: 33124 Cov.: 32

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.654 AC: 99303 AN: 151904 Hom.: 33147 Cov.: 32 AF XY: 0.652 AC XY: 48392 AN XY: 74228

Gnomad4 AFR AF: 0.815

Gnomad4 AMR AF: 0.598

Gnomad4 ASJ AF: 0.595

Gnomad4 EAS AF: 0.580

Gnomad4 SAS AF: 0.708

Gnomad4 FIN AF: 0.602

Gnomad4 NFE AF: 0.583

Gnomad4 OTH AF: 0.640

Alfa AF: 0.636 Hom.: 3914

Bravo AF: 0.652

Asia WGS AF: 0.702 AC: 2433 AN: 3470

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	0.23

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: rs1901062; hg19: chr8-106589534;