dbSNP rs71305140: ZFPM2:c.-65_-64insGGCGGCGGGAGCGGCGGGAGC (chr8-105318866-G-GGCGGCGGGAGCGGCGGCGGGA) – ACMG Classification: Likely_benign (-1 pts)

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BS2_Supporting

The NM_012082.4(ZFPM2):c.-65_-64insGGCGGCGGGAGCGGCGGGAGC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0000069 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0000074 ( 0 hom. )

Consequence

ZFPM2
NM_012082.4 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.37

Publications

1 publications found

Variant links:

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

ZFPM2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -1 ACMG points.

BS2

High AC in GnomAdExome4 at 5 AD,Unknown gene. Variant has AC lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZFPM2	NM_012082.4 link	c.-65_-64insGGCGGCGGGAGCGGCGGGAGC		5_prime_UTR_variant	Exon 1 of 8	ENST00000407775.7	NP_036214.2	Q8WW38-1Q9NPQ0
ZFPM2	NM_001362836.2 link	c.-65_-64insGGCGGCGGGAGCGGCGGGAGC		5_prime_UTR_variant	Exon 1 of 7		NP_001349765.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZFPM2	ENST00000407775.7 link	c.-65_-64insGGCGGCGGGAGCGGCGGGAGC		5_prime_UTR_variant	Exon 1 of 8	1	NM_012082.4	ENSP00000384179.2		Q8WW38-1
ZFPM2	ENST00000518180.1 link	n.479+72348_479+72349insGGCGGCGGGAGCGGCGGGAGC		intron_variant	Intron 4 of 4	4

Frequencies

GnomAD3 genomes

AF:

0.00000685

AC:

AN:

145902

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000679

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.00000742

AC:

AN:

674268

Hom.:

Cov.:

AF XY:

0.00000315

AC XY:

AN XY:

317362

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

11216

American (AMR)

AF:

0.00

AC:

AN:

1036

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

4266

East Asian (EAS)

AF:

0.00

AC:

AN:

3578

South Asian (SAS)

AF:

0.00

AC:

AN:

13836

European-Finnish (FIN)

AF:

0.00

AC:

AN:

7232

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1320

European-Non Finnish (NFE)

AF:

0.00000656

AC:

AN:

609922

Other (OTH)

AF:

0.0000457

AC:

AN:

21862

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.405

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.00000685

AC:

AN:

145902

Hom.:

Cov.:

AF XY:

0.0000141

AC XY:

AN XY:

70868

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

40682

American (AMR)

AF:

0.0000679

AC:

AN:

14722

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3382

East Asian (EAS)

AF:

0.00

AC:

AN:

4824

South Asian (SAS)

AF:

0.00

AC:

AN:

4790

European-Finnish (FIN)

AF:

0.00

AC:

AN:

8566

Middle Eastern (MID)

AF:

0.00

AC:

AN:

306

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

65704

Other (OTH)

AF:

0.00

AC:

AN:

2022

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00

Hom.:

1334

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

3.4

Splicing

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

Publications

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rs71305140

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over