Variant rs1062270 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001308093.3(GATA4):c.*1355G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0477 in 152,532 control chromosomes in the GnomAD database, including 255 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.048 ( 255 hom., cov: 33)

Exomes 𝑓: 0.060 ( 0 hom. )

Consequence

GATA4
NM_001308093.3 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.63

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

BP6

Variant 8-11759830-G-A is Benign according to our data. Variant chr8-11759830-G-A is described in ClinVar as [Benign]. Clinvar id is 1244459.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-11759830-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GATA4	NM_001308093.3 linkuse as main transcript	c.*1355G>A		3_prime_UTR_variant	7/7	ENST00000532059.6

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GATA4	ENST00000532059.6 linkuse as main transcript	c.*1355G>A	3_prime_UTR_variant	7/7	1	NM_001308093.3	A1	P43694-2
GATA4	ENST00000335135.8 linkuse as main transcript	c.*1355G>A	3_prime_UTR_variant	7/7	5		P3	P43694-1
GATA4	ENST00000528712.5 linkuse as main transcript	c.*1355G>A	3_prime_UTR_variant	7/7	2
GATA4	ENST00000622443.3 linkuse as main transcript	c.*1355G>A	3_prime_UTR_variant	8/8	5		P3	P43694-1

Frequencies

GnomAD3 genomes

AF:

0.0477

AC:

7256

AN:

152164

Hom.:

255

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0133

Gnomad AMI

AF:

0.326

Gnomad AMR

AF:

0.0504

Gnomad ASJ

AF:

0.0528

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00704

Gnomad FIN

AF:

0.0659

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0678

Gnomad OTH

AF:

0.0449

GnomAD4 exome

AF:

0.0600

AC:

AN:

250

Hom.:

Cov.:

AF XY:

0.0811

AC XY:

AN XY:

148

show subpopulations

Gnomad4 FIN exome

AF:

0.0565

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.143

GnomAD4 genome

AF:

0.0477

AC:

7257

AN:

152282

Hom.:

255

Cov.:

AF XY:

0.0468

AC XY:

3480

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.0132

Gnomad4 AMR

AF:

0.0503

Gnomad4 ASJ

AF:

0.0528

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00725

Gnomad4 FIN

AF:

0.0659

Gnomad4 NFE

AF:

0.0679

Gnomad4 OTH

AF:

0.0444

Alfa

AF:

0.0621

Hom.:

Bravo

AF:

0.0472

Asia WGS

AF:

0.00549

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 18, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

DANN

Benign

0.77

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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