rs71305152

Variant names:

• chr8-105437494-A-ATTTTCT
• rs71305152
• NM_012082.4:c.200-6785_200-6780dupTTTTCT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_012082.4(ZFPM2):​c.200-6785_200-6780dupTTTTCT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.42 (14872 hom., cov: 0)
• Consequence: ZFPM2 NM_012082.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.104
• Publications: 1 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: Labcorp Genetics (formerly Invitae), G2P
• 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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZFPM2	NM_012082.4	c.200-6785_200-6780dupTTTTCT		intron_variant	Intron 2 of 7	ENST00000407775.7	NP_036214.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZFPM2	ENST00000407775.7	c.200-6785_200-6780dupTTTTCT		intron_variant	Intron 2 of 7	1	NM_012082.4	ENSP00000384179.2

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64275 AN: 151348 Hom.: 14844 Cov.: 0

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.425 AC: 64369 AN: 151466 Hom.: 14872 Cov.: 0 AF XY: 0.428 AC XY: 31637 AN XY: 74000

African (AFR) AF: 0.622 AC: 25586 AN: 41158

American (AMR) AF: 0.420 AC: 6396 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1113 AN: 3456

East Asian (EAS) AF: 0.316 AC: 1624 AN: 5140

South Asian (SAS) AF: 0.419 AC: 2012 AN: 4802

European-Finnish (FIN) AF: 0.410 AC: 4302 AN: 10498

Middle Eastern (MID) AF: 0.315 AC: 92 AN: 292

European-Non Finnish (NFE) AF: 0.329 AC: 22345 AN: 67870

Other (OTH) AF: 0.377 AC: 793 AN: 2106

Alfa AF: 0.386 Hom.: 1240

Asia WGS AF: 0.407 AC: 1418 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.10
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs71305152; hg19: chr8-106449722;