rs7006733

Variant summary

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

The NM_001308093.3(GATA4):​c.912+245G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.743 in 152,228 control chromosomes in the GnomAD database, including 43,086 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.74 ( 43086 hom., cov: 33)

Consequence

GATA4
NM_001308093.3 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.54
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]

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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=-1.0).
BP6
Variant 8-11750481-G-A is Benign according to our data. Variant chr8-11750481-G-A is described in ClinVar as [Benign]. Clinvar id is 1293502.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
GATA4NM_001308093.3 linkuse as main transcriptc.912+245G>A intron_variant ENST00000532059.6 NP_001295022.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
GATA4ENST00000532059.6 linkuse as main transcriptc.912+245G>A intron_variant 1 NM_001308093.3 ENSP00000435712 A1P43694-2

Frequencies

GnomAD3 genomes
AF:
0.743
AC:
113005
AN:
152108
Hom.:
43031
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.871
Gnomad AMI
AF:
0.596
Gnomad AMR
AF:
0.770
Gnomad ASJ
AF:
0.572
Gnomad EAS
AF:
0.982
Gnomad SAS
AF:
0.785
Gnomad FIN
AF:
0.798
Gnomad MID
AF:
0.674
Gnomad NFE
AF:
0.642
Gnomad OTH
AF:
0.693
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.743
AC:
113120
AN:
152228
Hom.:
43086
Cov.:
33
AF XY:
0.754
AC XY:
56118
AN XY:
74412
show subpopulations
Gnomad4 AFR
AF:
0.871
Gnomad4 AMR
AF:
0.771
Gnomad4 ASJ
AF:
0.572
Gnomad4 EAS
AF:
0.982
Gnomad4 SAS
AF:
0.783
Gnomad4 FIN
AF:
0.798
Gnomad4 NFE
AF:
0.642
Gnomad4 OTH
AF:
0.696
Alfa
AF:
0.663
Hom.:
13862
Bravo
AF:
0.744
Asia WGS
AF:
0.901
AC:
3131
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 submitterclinical testingGeneDxSep 04, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.11
DANN
Benign
0.54

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.

Other links and lift over

dbSNP: rs7006733; hg19: chr8-11607990; API