rs1460239

Variant names:

• chr8-104799137-C-T
• rs1460239
• ENST00000518180.1:n.196+84162C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000521923.5(ZFPM2):​n.167-28220C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 151,984 control chromosomes in the GnomAD database, including 18,899 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 0.49 (18899 hom., cov: 33)
• Consequence: ZFPM2 ENST00000521923.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.224
• Publications: 3 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 Gene-Disease associations (from GenCC):

• 46,XY sex reversal 9

  Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• diaphragmatic hernia 3

  Inheritance: AD Classification: STRONG, LIMITED Submitted by: G2P, Labcorp Genetics (formerly Invitae)
• tetralogy of fallot

  Inheritance: Unknown, AD Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
• 46,XY partial gonadal dysgenesis

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000521923.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFPM2	ENST00000518180.1	TSL:4	n.196+84162C>T		intron	N/A
	ZFPM2	ENST00000521923.5	TSL:3	n.167-28220C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73768 AN: 151866 Hom.: 18897 Cov.: 33

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.486 AC: 73794 AN: 151984 Hom.: 18899 Cov.: 33 AF XY: 0.483 AC XY: 35835 AN XY: 74268

African (AFR) AF: 0.346 AC: 14331 AN: 41454

American (AMR) AF: 0.530 AC: 8101 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1662 AN: 3470

East Asian (EAS) AF: 0.235 AC: 1213 AN: 5170

South Asian (SAS) AF: 0.571 AC: 2749 AN: 4816

European-Finnish (FIN) AF: 0.486 AC: 5120 AN: 10542

Middle Eastern (MID) AF: 0.551 AC: 161 AN: 292

European-Non Finnish (NFE) AF: 0.571 AC: 38774 AN: 67938

Other (OTH) AF: 0.507 AC: 1071 AN: 2114

Alfa AF: 0.544 Hom.: 12638

Bravo AF: 0.481

Asia WGS AF: 0.389 AC: 1354 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	18
DANN	Benign	0.70
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs1460239; hg19: chr8-105811365;