NM_012082.4:c.2976T>C

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.2976T>C(p.Tyr992Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0298 in 1,613,690 control chromosomes in the GnomAD database, including 1,358 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.055 ( 456 hom., cov: 32)

Exomes 𝑓: 0.027 ( 902 hom. )

Consequence

ZFPM2
NM_012082.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.493

Publications

8 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=-0.79).

BP6

Variant 8-105803058-T-C is Benign according to our data. Variant chr8-105803058-T-C is described in ClinVar as Benign. ClinVar VariationId is 260176.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.493 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZFPM2	NM_012082.4 link	c.2976T>C	p.Tyr992Tyr	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.2976T>C	p.Tyr992Tyr	synonymous_variant	Exon 8 of 8	1	NM_012082.4	ENSP00000384179.2		Q8WW38-1

Frequencies

GnomAD3 genomes

AF:

0.0553

AC:

8417

AN:

152126

Hom.:

451

Cov.:

show subpopulations

Gnomad AFR

AF:

0.134

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.0524

Gnomad ASJ

AF:

0.0686

Gnomad EAS

AF:

0.00790

Gnomad SAS

AF:

0.0306

Gnomad FIN

AF:

0.00433

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0211

Gnomad OTH

AF:

0.0608

GnomAD2 exomes

AF:

0.0313

AC:

7787

AN:

248408

AF XY:

0.0294

show subpopulations

Gnomad AFR exome

AF:

0.135

Gnomad AMR exome

AF:

0.0307

Gnomad ASJ exome

AF:

0.0717

Gnomad EAS exome

AF:

0.00688

Gnomad FIN exome

AF:

0.00446

Gnomad NFE exome

AF:

0.0220

Gnomad OTH exome

AF:

0.0345

GnomAD4 exome

AF:

0.0271

AC:

39595

AN:

1461446

Hom.:

902

Cov.:

AF XY:

0.0267

AC XY:

19442

AN XY:

726980

show subpopulations

African (AFR)

AF:

0.142

AC:

4751

AN:

33472

American (AMR)

AF:

0.0331

AC:

1480

AN:

44676

Ashkenazi Jewish (ASJ)

AF:

0.0703

AC:

1835

AN:

26108

East Asian (EAS)

AF:

0.00459

AC:

182

AN:

39668

South Asian (SAS)

AF:

0.0302

AC:

2601

AN:

86232

European-Finnish (FIN)

AF:

0.00545

AC:

291

AN:

53390

Middle Eastern (MID)

AF:

0.0331

AC:

191

AN:

5766

European-Non Finnish (NFE)

AF:

0.0234

AC:

26028

AN:

1111768

Other (OTH)

AF:

0.0370

AC:

2236

AN:

60366

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

2496

4992

7489

9985

12481

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1116

2232

3348

4464

5580

<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:

0.0555

AC:

8447

AN:

152244

Hom.:

456

Cov.:

AF XY:

0.0540

AC XY:

4021

AN XY:

74470

show subpopulations

African (AFR)

AF:

0.135

AC:

5601

AN:

41522

American (AMR)

AF:

0.0523

AC:

799

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0686

AC:

238

AN:

3468

East Asian (EAS)

AF:

0.00773

AC:

AN:

5176

South Asian (SAS)

AF:

0.0302

AC:

146

AN:

4832

European-Finnish (FIN)

AF:

0.00433

AC:

AN:

10622

Middle Eastern (MID)

AF:

0.0306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0211

AC:

1436

AN:

68018

Other (OTH)

AF:

0.0607

AC:

128

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

389

778

1168

1557

1946

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

188

282

376

470

<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:

0.0347

Hom.:

425

Bravo

AF:

0.0633

Asia WGS

AF:

0.0550

AC:

190

AN:

3478

EpiCase

AF:

0.0256

EpiControl

AF:

0.0256

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Jul 03, 2023

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

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

- -

Mar 16, 2021

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

-0.79

CADD

Benign

0.68

(source)

DANN

Benign

0.55

PhyloP100

-0.49

Mutation Taster

=91/9

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