rs1062270
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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
NM_001308093.3 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.63
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=-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 | c.*1355G>A | 3_prime_UTR_variant | 7/7 | ENST00000532059.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GATA4 | ENST00000532059.6 | c.*1355G>A | 3_prime_UTR_variant | 7/7 | 1 | NM_001308093.3 | A1 | ||
GATA4 | ENST00000335135.8 | c.*1355G>A | 3_prime_UTR_variant | 7/7 | 5 | P3 | |||
GATA4 | ENST00000528712.5 | c.*1355G>A | 3_prime_UTR_variant | 7/7 | 2 | ||||
GATA4 | ENST00000622443.3 | c.*1355G>A | 3_prime_UTR_variant | 8/8 | 5 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0477 AC: 7256AN: 152164Hom.: 255 Cov.: 33
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GnomAD4 exome AF: 0.0600 AC: 15AN: 250Hom.: 0 Cov.: 0 AF XY: 0.0811 AC XY: 12AN XY: 148
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GnomAD4 genome ? AF: 0.0477 AC: 7257AN: 152282Hom.: 255 Cov.: 33 AF XY: 0.0468 AC XY: 3480AN XY: 74438
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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
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at