rs920628

Variant names:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_012082.4(ZFPM2):c.1362A>G(p.Pro454Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0406 in 1,613,784 control chromosomes in the GnomAD database, including 5,110 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 2406 hom., cov: 32)

Exomes 𝑓: 0.033 ( 2704 hom. )

Consequence

ZFPM2
NM_012082.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -0.167

Publications

5 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 links:

ZFPM2-AS1 (HGNC:50698): (ZFPM2 antisense RNA 1)

ZFPM2-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.7).

BP6

Variant 8-105801444-A-G is Benign according to our data. Variant chr8-105801444-A-G is described in ClinVar as Benign. ClinVar VariationId is 260171.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.167 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZFPM2	NM_012082.4 link	c.1362A>G	p.Pro454Pro	synonymous_variant	Exon 8 of 8	ENST00000407775.7	NP_036214.2	Q8WW38-1Q9NPQ0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZFPM2	ENST00000407775.7 link	c.1362A>G	p.Pro454Pro	synonymous_variant	Exon 8 of 8	1	NM_012082.4	ENSP00000384179.2		Q8WW38-1

Frequencies

GnomAD3 genomes

AF:

0.112

AC:

17092

AN:

152026

Hom.:

2387

Cov.:

show subpopulations

Gnomad AFR

AF:

0.332

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.0786

Gnomad ASJ

AF:

0.0709

Gnomad EAS

AF:

0.00790

Gnomad SAS

AF:

0.0330

Gnomad FIN

AF:

0.00414

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0219

Gnomad OTH

AF:

0.0967

GnomAD2 exomes

AF:

0.0462

AC:

11487

AN:

248804

AF XY:

0.0406

show subpopulations

Gnomad AFR exome

AF:

0.338

Gnomad AMR exome

AF:

0.0423

Gnomad ASJ exome

AF:

0.0727

Gnomad EAS exome

AF:

0.00693

Gnomad FIN exome

AF:

0.00446

Gnomad NFE exome

AF:

0.0226

Gnomad OTH exome

AF:

0.0417

GnomAD4 exome

AF:

0.0331

AC:

48333

AN:

1461640

Hom.:

2704

Cov.:

AF XY:

0.0319

AC XY:

23197

AN XY:

727102

show subpopulations

African (AFR)

AF:

0.342

AC:

11444

AN:

33478

American (AMR)

AF:

0.0459

AC:

2050

AN:

44708

Ashkenazi Jewish (ASJ)

AF:

0.0714

AC:

1865

AN:

26134

East Asian (EAS)

AF:

0.00461

AC:

183

AN:

39692

South Asian (SAS)

AF:

0.0307

AC:

2644

AN:

86252

European-Finnish (FIN)

AF:

0.00547

AC:

292

AN:

53398

Middle Eastern (MID)

AF:

0.0439

AC:

253

AN:

5768

European-Non Finnish (NFE)

AF:

0.0238

AC:

26504

AN:

1111838

Other (OTH)

AF:

0.0513

AC:

3098

AN:

60372

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

3210

6419

9629

12838

16048

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1226

2452

3678

4904

6130

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.113

AC:

17156

AN:

152144

Hom.:

2406

Cov.:

AF XY:

0.109

AC XY:

8093

AN XY:

74398

show subpopulations

African (AFR)

AF:

0.332

AC:

13766

AN:

41432

American (AMR)

AF:

0.0784

AC:

1199

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0709

AC:

246

AN:

3472

East Asian (EAS)

AF:

0.00772

AC:

AN:

5178

South Asian (SAS)

AF:

0.0322

AC:

155

AN:

4820

European-Finnish (FIN)

AF:

0.00414

AC:

AN:

10620

Middle Eastern (MID)

AF:

0.0442

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0218

AC:

1486

AN:

68020

Other (OTH)

AF:

0.0962

AC:

203

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

643

1285

1928

2570

3213

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

160

320

480

640

800

<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:

0.0579

Hom.:

2688

Bravo

AF:

0.128

Asia WGS

AF:

0.0670

AC:

234

AN:

3478

EpiCase

AF:

0.0261

EpiControl

AF:

0.0264

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Apr 10, 2023

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Sep 17, 2019

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

46,XY sex reversal 9

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

0.14

(source)

DANN

Benign

0.55

PhyloP100

-0.17

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over