rs10505082

Variant names:

• chr8-105768400-G-A
• rs10505082
• NM_012082.4:c.533-20318G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012082.4(ZFPM2):​c.533-20318G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 151,724 control chromosomes in the GnomAD database, including 7,375 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 0.27 (7375 hom., cov: 32)
• Consequence: ZFPM2 NM_012082.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.814
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZFPM2	NM_012082.4	c.533-20318G>A		intron_variant	Intron 5 of 7	ENST00000407775.7	NP_036214.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZFPM2	ENST00000407775.7	c.533-20318G>A		intron_variant	Intron 5 of 7	1	NM_012082.4	ENSP00000384179.2

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41536 AN: 151606 Hom.: 7349 Cov.: 32

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.274 AC: 41620 AN: 151724 Hom.: 7375 Cov.: 32 AF XY: 0.273 AC XY: 20260 AN XY: 74140

African (AFR) AF: 0.490 AC: 20286 AN: 41416

American (AMR) AF: 0.273 AC: 4147 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 551 AN: 3466

East Asian (EAS) AF: 0.414 AC: 2126 AN: 5134

South Asian (SAS) AF: 0.134 AC: 646 AN: 4814

European-Finnish (FIN) AF: 0.177 AC: 1876 AN: 10584

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11262 AN: 67824

Other (OTH) AF: 0.255 AC: 536 AN: 2104

Alfa AF: 0.205 Hom.: 5706

Bravo AF: 0.293

Asia WGS AF: 0.329 AC: 1143 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.053
DANN	Benign	0.20
PhyloP100		-0.81
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10505082; hg19: chr8-106780628;