8-105561350-C-T

Variant names:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_012082.4(ZFPM2):c.302-13C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.604 in 1,606,566 control chromosomes in the GnomAD database, including 298,307 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.68 ( 36535 hom., cov: 32)

Exomes 𝑓: 0.60 ( 261772 hom. )

Consequence

ZFPM2
NM_012082.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: 0.911

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.55).

BP6

Variant 8-105561350-C-T is Benign according to our data. Variant chr8-105561350-C-T is described in ClinVar as [Benign]. Clinvar id is 260177.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-105561350-C-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZFPM2	NM_012082.4 link	c.302-13C>T		intron_variant	Intron 3 of 7	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.302-13C>T		intron_variant	Intron 3 of 7	1	NM_012082.4	ENSP00000384179.2		Q8WW38-1

Frequencies

GnomAD3 genomes

AF:

0.679

AC:

103056

AN:

151884

Hom.:

36499

Cov.:

show subpopulations

Gnomad AFR

AF:

0.911

Gnomad AMI

AF:

0.499

Gnomad AMR

AF:

0.613

Gnomad ASJ

AF:

0.616

Gnomad EAS

AF:

0.595

Gnomad SAS

AF:

0.713

Gnomad FIN

AF:

0.572

Gnomad MID

AF:

0.652

Gnomad NFE

AF:

0.579

Gnomad OTH

AF:

0.654

GnomAD3 exomes

AF:

0.618

AC:

152047

AN:

245868

Hom.:

48011

AF XY:

0.621

AC XY:

82725

AN XY:

133294

show subpopulations

Gnomad AFR exome

AF:

0.917

Gnomad AMR exome

AF:

0.564

Gnomad ASJ exome

AF:

0.599

Gnomad EAS exome

AF:

0.597

Gnomad SAS exome

AF:

0.727

Gnomad FIN exome

AF:

0.564

Gnomad NFE exome

AF:

0.580

Gnomad OTH exome

AF:

0.614

GnomAD4 exome

AF:

0.596

AC:

867033

AN:

1454564

Hom.:

261772

Cov.:

AF XY:

0.599

AC XY:

433865

AN XY:

723860

show subpopulations

Gnomad4 AFR exome

AF:

0.923

Gnomad4 AMR exome

AF:

0.565

Gnomad4 ASJ exome

AF:

0.601

Gnomad4 EAS exome

AF:

0.553

Gnomad4 SAS exome

AF:

0.720

Gnomad4 FIN exome

AF:

0.576

Gnomad4 NFE exome

AF:

0.578

Gnomad4 OTH exome

AF:

0.623

GnomAD4 genome

AF:

0.679

AC:

103147

AN:

152002

Hom.:

36535

Cov.:

AF XY:

0.675

AC XY:

50127

AN XY:

74270

show subpopulations

Gnomad4 AFR

AF:

0.911

Gnomad4 AMR

AF:

0.613

Gnomad4 ASJ

AF:

0.616

Gnomad4 EAS

AF:

0.595

Gnomad4 SAS

AF:

0.711

Gnomad4 FIN

AF:

0.572

Gnomad4 NFE

AF:

0.579

Gnomad4 OTH

AF:

0.658

Alfa

AF:

0.595

Hom.:

46322

Bravo

AF:

0.684

Asia WGS

AF:

0.723

AC:

2510

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:8

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Apr 04, 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

- -

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

46,XY sex reversal 9

Benign:2

Dec 05, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:2

Nov 13, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Tetralogy of Fallot

Benign:1

Dec 05, 2021

Genome-Nilou Lab

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

-0.55

CADD

Benign

9.9

DANN

Benign

0.66

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