chr8-105569056-G-A

Variant names:

• chr8-105569056-G-A
• rs6993696
• NM_012082.4:c.420+7575G>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+7575G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 151,340 control chromosomes in the GnomAD database, including 15,364 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 0.45 (15364 hom., cov: 29)
• Consequence: ZFPM2 NM_012082.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.503
• Publications: 7 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZFPM2	NM_012082.4	c.420+7575G>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+7575G>A		intron_variant	Intron 4 of 7	1	NM_012082.4	ENSP00000384179.2

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68109 AN: 151224 Hom.: 15357 Cov.: 29

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.450 AC: 68143 AN: 151340 Hom.: 15364 Cov.: 29 AF XY: 0.443 AC XY: 32768 AN XY: 73906

African (AFR) AF: 0.509 AC: 20954 AN: 41164

American (AMR) AF: 0.393 AC: 5976 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1798 AN: 3464

East Asian (EAS) AF: 0.449 AC: 2301 AN: 5122

South Asian (SAS) AF: 0.489 AC: 2347 AN: 4800

European-Finnish (FIN) AF: 0.345 AC: 3604 AN: 10452

Middle Eastern (MID) AF: 0.455 AC: 133 AN: 292

European-Non Finnish (NFE) AF: 0.439 AC: 29799 AN: 67844

Other (OTH) AF: 0.464 AC: 972 AN: 2094

Alfa AF: 0.450 Hom.: 8100

Bravo AF: 0.452

Asia WGS AF: 0.497 AC: 1726 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.25
DANN	Benign	0.45
PhyloP100		-0.50
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: rs6993696; hg19: chr8-106581284;