rs11995760

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_012082.4(ZFPM2):c.3207C>T(p.His1069=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0404 in 1,594,158 control chromosomes in the GnomAD database, including 5,053 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 2412 hom., cov: 32)

Exomes 𝑓: 0.033 ( 2641 hom. )

Consequence

ZFPM2
NM_012082.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.197

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 made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 8-105803289-C-T is Benign according to our data. Variant chr8-105803289-C-T is described in ClinVar as [Benign]. Clinvar id is 260178.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-105803289-C-T is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=0.197 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.327 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZFPM2	NM_012082.4 linkuse as main transcript	c.3207C>T	p.His1069=	synonymous_variant	8/8	ENST00000407775.7
ZFPM2-AS1	NR_125797.1 linkuse as main transcript	n.191-4847G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZFPM2	ENST00000407775.7 linkuse as main transcript	c.3207C>T	p.His1069=	synonymous_variant	8/8	1	NM_012082.4	P1	Q8WW38-1
ZFPM2-AS1	ENST00000520433.5 linkuse as main transcript	n.212-4847G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.113

AC:

17115

AN:

152026

Hom.:

2393

Cov.:

show subpopulations

Gnomad AFR

AF:

0.331

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.0814

Gnomad ASJ

AF:

0.0706

Gnomad EAS

AF:

0.00792

Gnomad SAS

AF:

0.0329

Gnomad FIN

AF:

0.00424

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0217

Gnomad OTH

AF:

0.0957

GnomAD3 exomes

AF:

0.0472

AC:

11005

AN:

233362

Hom.:

1028

AF XY:

0.0414

AC XY:

5217

AN XY:

126002

show subpopulations

Gnomad AFR exome

AF:

0.337

Gnomad AMR exome

AF:

0.0436

Gnomad ASJ exome

AF:

0.0747

Gnomad EAS exome

AF:

0.00689

Gnomad SAS exome

AF:

0.0365

Gnomad FIN exome

AF:

0.00432

Gnomad NFE exome

AF:

0.0224

Gnomad OTH exome

AF:

0.0417

GnomAD4 exome

AF:

0.0328

AC:

47262

AN:

1442014

Hom.:

2641

Cov.:

AF XY:

0.0317

AC XY:

22644

AN XY:

714944

show subpopulations

Gnomad4 AFR exome

AF:

0.341

Gnomad4 AMR exome

AF:

0.0473

Gnomad4 ASJ exome

AF:

0.0712

Gnomad4 EAS exome

AF:

0.00464

Gnomad4 SAS exome

AF:

0.0309

Gnomad4 FIN exome

AF:

0.00538

Gnomad4 NFE exome

AF:

0.0236

Gnomad4 OTH exome

AF:

0.0508

GnomAD4 genome

AF:

0.113

AC:

17179

AN:

152144

Hom.:

2412

Cov.:

AF XY:

0.109

AC XY:

8127

AN XY:

74390

show subpopulations

Gnomad4 AFR

AF:

0.332

Gnomad4 AMR

AF:

0.0812

Gnomad4 ASJ

AF:

0.0706

Gnomad4 EAS

AF:

0.00774

Gnomad4 SAS

AF:

0.0321

Gnomad4 FIN

AF:

0.00424

Gnomad4 NFE

AF:

0.0217

Gnomad4 OTH

AF:

0.0952

Alfa

AF:

0.0488

Hom.:

803

Bravo

AF:

0.128

Asia WGS

AF:

0.0670

AC:

234

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Apr 10, 2023	- -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -

46,XY sex reversal 9

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

Cadd

Benign

0.39

Dann

Benign

0.80

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over