Variant rs867858 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001308093.3(GATA4):c.*354A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 352,036 control chromosomes in the GnomAD database, including 19,148 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).

Frequency

Genomes: 𝑓 0.30 ( 7205 hom., cov: 32)

Exomes 𝑓: 0.34 ( 11943 hom. )

Consequence

GATA4
NM_001308093.3 3_prime_UTR

Scores

Clinical Significance

Uncertain significance no assertion criteria provided U:1

Conservation

PhyloP100: -0.602

Variant links:

Genes affected

GATA4 (HGNC:4173): (GATA binding protein 4) This gene encodes a member of the GATA family of zinc-finger transcription factors. Members of this family recognize the GATA motif which is present in the promoters of many genes. This protein is thought to regulate genes involved in embryogenesis and in myocardial differentiation and function, and is necessary for normal testicular development. Mutations in this gene have been associated with cardiac septal defects. Additionally, alterations in gene expression have been associated with several cancer types. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]

GATA4 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GATA4	NM_001308093.3 linkuse as main transcript	c.*354A>C		3_prime_UTR_variant	7/7	ENST00000532059.6	NP_001295022.1	P43694-2B3KUF4B6DU75

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
GATA4	ENST00000532059.6 linkuse as main transcript	c.*354A>C	3_prime_UTR_variant	7/7	1	NM_001308093.3	ENSP00000435712.1	P43694-2
GATA4	ENST00000335135.8 linkuse as main transcript	c.*354A>C	3_prime_UTR_variant	7/7	5		ENSP00000334458.4	P43694-1
GATA4	ENST00000622443.3 linkuse as main transcript	c.*354A>C	3_prime_UTR_variant	8/8	5		ENSP00000482268.2	P43694-1A0A087WZ09
GATA4	ENST00000528712.5 linkuse as main transcript	c.*354A>C	3_prime_UTR_variant	7/7	2		ENSP00000435043.1	B3KUF4

Frequencies

GnomAD3 genomes

AF:

0.300

AC:

45519

AN:

151798

Hom.:

7204

Cov.:

show subpopulations

Gnomad AFR

AF:

0.225

Gnomad AMI

AF:

0.326

Gnomad AMR

AF:

0.314

Gnomad ASJ

AF:

0.337

Gnomad EAS

AF:

0.559

Gnomad SAS

AF:

0.385

Gnomad FIN

AF:

0.303

Gnomad MID

AF:

0.377

Gnomad NFE

AF:

0.313

Gnomad OTH

AF:

0.321

GnomAD4 exome

AF:

0.337

AC:

67505

AN:

200120

Hom.:

11943

Cov.:

AF XY:

0.345

AC XY:

37101

AN XY:

107552

show subpopulations

Gnomad4 AFR exome

AF:

0.241

Gnomad4 AMR exome

AF:

0.318

Gnomad4 ASJ exome

AF:

0.329

Gnomad4 EAS exome

AF:

0.543

Gnomad4 SAS exome

AF:

0.386

Gnomad4 FIN exome

AF:

0.316

Gnomad4 NFE exome

AF:

0.316

Gnomad4 OTH exome

AF:

0.330

GnomAD4 genome

AF:

0.300

AC:

45528

AN:

151916

Hom.:

7205

Cov.:

AF XY:

0.305

AC XY:

22641

AN XY:

74260

show subpopulations

Gnomad4 AFR

AF:

0.224

Gnomad4 AMR

AF:

0.313

Gnomad4 ASJ

AF:

0.337

Gnomad4 EAS

AF:

0.559

Gnomad4 SAS

AF:

0.385

Gnomad4 FIN

AF:

0.303

Gnomad4 NFE

AF:

0.313

Gnomad4 OTH

AF:

0.321

Alfa

AF:

0.314

Hom.:

10160

Bravo

AF:

0.295

Asia WGS

AF:

0.460

AC:

1598

AN:

3478

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

not provided

Uncertain:1

Uncertain significance, no assertion criteria provided

literature only

Molecular Genetics and Enzymology, National Research Centre

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

1.5

DANN

Benign

0.42

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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