8-105318866-G-GGCGGCGGGA

Position:

• chr8-105318866-G-GGCGGCGGGA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_012082.4(ZFPM2):​c.-73_-65dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.84 (51088 hom., cov: 0)
  • Exomes 𝑓: 0.76 (187936 hom.)
• Consequence: ZFPM2 NM_012082.4 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 3.37

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 8-105318866-G-GGCGGCGGGA is Benign according to our data. Variant chr8-105318866-G-GGCGGCGGGA is described in ClinVar as [Benign]. Clinvar id is 1233669.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.923 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZFPM2	NM_012082.4	c.-73_-65dup		5_prime_UTR_variant	1/8	ENST00000407775.7	NP_036214.2
ZFPM2	NM_001362836.2	c.-73_-65dup		5_prime_UTR_variant	1/7		NP_001349765.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZFPM2	ENST00000407775.7	c.-73_-65dup		5_prime_UTR_variant	1/8	1	NM_012082.4	ENSP00000384179	P1
ZFPM2	ENST00000518180.1	n.479+72340_479+72348dup		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.836 AC: 121884 AN: 145846 Hom.: 51051 Cov.: 0

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.877

Gnomad AMR AF: 0.873

Gnomad ASJ AF: 0.844

Gnomad EAS AF: 0.947

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.888

Gnomad MID AF: 0.876

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.849

GnomAD4 exome AF: 0.755 AC: 506434 AN: 670558 Hom.: 187936 Cov.: 13 AF XY: 0.754 AC XY: 237842 AN XY: 315646

Gnomad4 AFR exome AF: 0.787

Gnomad4 AMR exome AF: 0.784

Gnomad4 ASJ exome AF: 0.784

Gnomad4 EAS exome AF: 0.869

Gnomad4 SAS exome AF: 0.798

Gnomad4 FIN exome AF: 0.824

Gnomad4 NFE exome AF: 0.751

Gnomad4 OTH exome AF: 0.772

GnomAD4 genome AF: 0.836 AC: 121967 AN: 145942 Hom.: 51088 Cov.: 0 AF XY: 0.841 AC XY: 59679 AN XY: 70954

Gnomad4 AFR AF: 0.824

Gnomad4 AMR AF: 0.873

Gnomad4 ASJ AF: 0.844

Gnomad4 EAS AF: 0.946

Gnomad4 SAS AF: 0.881

Gnomad4 FIN AF: 0.888

Gnomad4 NFE AF: 0.815

Gnomad4 OTH AF: 0.848

Alfa AF: 0.703 Hom.: 1334

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs71305140; hg19: chr8-106331094;