dbSNP rs71305152: ZFPM2:c.200-6785_200-6780dupTTTTCT (chr8-105437494-A-ATTTTCT) – ACMG Classification: Benign (-8 pts)

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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.104

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

new If you want to explore the variant's impact on the transcript NM_012082.4, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012082.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZFPM2	NM_012082.4	MANE Select	c.200-6785_200-6780dupTTTTCT	intron	N/A	NP_036214.2	Q8WW38-1
ZFPM2	NM_001362836.2		c.41-6785_41-6780dupTTTTCT	intron	N/A	NP_001349765.1
ZFPM2	NM_001362837.2		c.-197-6785_-197-6780dupTTTTCT	intron	N/A	NP_001349766.1	E7ET52

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZFPM2	ENST00000407775.7	TSL:1 MANE Select	c.200-6786_200-6785insTTTTCT	intron	N/A	ENSP00000384179.2	Q8WW38-1
ZFPM2	ENST00000511341.6	TSL:1	n.940-6786_940-6785insTTTTCT	intron	N/A
ZFPM2	ENST00000941376.1		c.200-6786_200-6785insTTTTCT	intron	N/A	ENSP00000611435.1

Frequencies

GnomAD3 genomes

AF:

0.425

AC:

64275

AN:

151348

Hom.:

14844

Cov.:

show subpopulations

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.:

AF XY:

0.428

AC XY:

31637

AN XY:

74000

show subpopulations

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:

AN:

292

European-Non Finnish (NFE)

AF:

0.329

AC:

22345

AN:

67870

Other (OTH)

AF:

0.377

AC:

793

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1766

3532

5297

7063

8829

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

574

1148

1722

2296

2870

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.386

Hom.:

1240

Asia WGS

AF:

0.407

AC:

1418

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.10

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over