chr8-105581330-G-A

Variant names:

• chr8-105581330-G-A
• rs7013321
• NM_012082.4:c.420+19849G>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.420+19849G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 152,004 control chromosomes in the GnomAD database, including 20,260 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 0.51 (20260 hom., cov: 32)
• Consequence: ZFPM2 NM_012082.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.398
• Publications: 4 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZFPM2	NM_012082.4	c.420+19849G>A		intron_variant	Intron 4 of 7	ENST00000407775.7	NP_036214.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZFPM2	ENST00000407775.7	c.420+19849G>A		intron_variant	Intron 4 of 7	1	NM_012082.4	ENSP00000384179.2

Frequencies

GnomAD3 genomes AF: 0.507 AC: 77070 AN: 151886 Hom.: 20258 Cov.: 32

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.507 AC: 77106 AN: 152004 Hom.: 20260 Cov.: 32 AF XY: 0.501 AC XY: 37175 AN XY: 74268

African (AFR) AF: 0.653 AC: 27080 AN: 41474

American (AMR) AF: 0.425 AC: 6479 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.515 AC: 1789 AN: 3472

East Asian (EAS) AF: 0.475 AC: 2460 AN: 5174

South Asian (SAS) AF: 0.529 AC: 2555 AN: 4830

European-Finnish (FIN) AF: 0.368 AC: 3882 AN: 10546

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31234 AN: 67932

Other (OTH) AF: 0.506 AC: 1067 AN: 2110

Alfa AF: 0.527 Hom.: 4567

Bravo AF: 0.512

Asia WGS AF: 0.501 AC: 1743 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.53
PhyloP100		0.40
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: rs7013321; hg19: chr8-106593558;