Variant rs35998713 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_012082.4(ZFPM2):c.2385C>G(p.Val795=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0296 in 1,613,404 control chromosomes in the GnomAD database, including 1,348 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.055 ( 455 hom., cov: 32)

Exomes 𝑓: 0.027 ( 893 hom. )

Consequence

ZFPM2
NM_012082.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.13

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=-0.56).

BP6

Variant 8-105802467-C-G is Benign according to our data. Variant chr8-105802467-C-G is described in ClinVar as [Benign]. Clinvar id is 260175.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.13 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/exons	MANE	Protein	UniProt
ZFPM2	NM_012082.4 linkuse as main transcript	c.2385C>G	p.Val795=	synonymous_variant	8/8	ENST00000407775.7	NP_036214.2
ZFPM2-AS1	NR_125797.1 linkuse as main transcript	n.191-4025G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZFPM2	ENST00000407775.7 linkuse as main transcript	c.2385C>G	p.Val795=	synonymous_variant	8/8	1	NM_012082.4	ENSP00000384179	P1	Q8WW38-1
ZFPM2-AS1	ENST00000520433.5 linkuse as main transcript	n.212-4025G>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.0553

AC:

8409

AN:

152140

Hom.:

450

Cov.:

show subpopulations

Gnomad AFR

AF:

0.135

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.0524

Gnomad ASJ

AF:

0.0685

Gnomad EAS

AF:

0.00791

Gnomad SAS

AF:

0.0282

Gnomad FIN

AF:

0.00433

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.0211

Gnomad OTH

AF:

0.0612

GnomAD3 exomes

AF:

0.0311

AC:

7681

AN:

247142

Hom.:

292

AF XY:

0.0291

AC XY:

3903

AN XY:

134114

show subpopulations

Gnomad AFR exome

AF:

0.135

Gnomad AMR exome

AF:

0.0307

Gnomad ASJ exome

AF:

0.0714

Gnomad EAS exome

AF:

0.00688

Gnomad SAS exome

AF:

0.0322

Gnomad FIN exome

AF:

0.00446

Gnomad NFE exome

AF:

0.0219

Gnomad OTH exome

AF:

0.0344

GnomAD4 exome

AF:

0.0269

AC:

39312

AN:

1461146

Hom.:

893

Cov.:

AF XY:

0.0265

AC XY:

19275

AN XY:

726768

show subpopulations

Gnomad4 AFR exome

AF:

0.142

Gnomad4 AMR exome

AF:

0.0330

Gnomad4 ASJ exome

AF:

0.0703

Gnomad4 EAS exome

AF:

0.00456

Gnomad4 SAS exome

AF:

0.0288

Gnomad4 FIN exome

AF:

0.00546

Gnomad4 NFE exome

AF:

0.0233

Gnomad4 OTH exome

AF:

0.0368

GnomAD4 genome

AF:

0.0554

AC:

8439

AN:

152258

Hom.:

455

Cov.:

AF XY:

0.0538

AC XY:

4006

AN XY:

74456

show subpopulations

Gnomad4 AFR

AF:

0.135

Gnomad4 AMR

AF:

0.0522

Gnomad4 ASJ

AF:

0.0685

Gnomad4 EAS

AF:

0.00773

Gnomad4 SAS

AF:

0.0278

Gnomad4 FIN

AF:

0.00433

Gnomad4 NFE

AF:

0.0211

Gnomad4 OTH

AF:

0.0610

Alfa

AF:

0.0249

Hom.:

Bravo

AF:

0.0632

Asia WGS

AF:

0.0540

AC:

188

AN:

3478

EpiCase

AF:

0.0254

EpiControl

AF:

0.0255

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jul 03, 2023	- -

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 09, 2019	- -

46,XY sex reversal 9

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

7.0

DANN

Benign

0.79

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