rs804290
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001308093.3(GATA4):c.*852G>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 0.161 in 152,750 control chromosomes in the GnomAD database, including 2,624 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001308093.3 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GATA4 | ENST00000532059.6 | c.*852G>A | 3_prime_UTR_variant | Exon 7 of 7 | 1 | NM_001308093.3 | ENSP00000435712.1 | |||
GATA4 | ENST00000335135.8 | c.*852G>A | 3_prime_UTR_variant | Exon 7 of 7 | 5 | ENSP00000334458.4 | ||||
GATA4 | ENST00000622443.3 | c.*852G>A | 3_prime_UTR_variant | Exon 8 of 8 | 5 | ENSP00000482268.2 | ||||
GATA4 | ENST00000528712.5 | c.*852G>A | 3_prime_UTR_variant | Exon 7 of 7 | 2 | ENSP00000435043.1 |
Frequencies
GnomAD3 genomes AF: 0.161 AC: 24477AN: 152116Hom.: 2614 Cov.: 33
GnomAD4 exome AF: 0.202 AC: 104AN: 516Hom.: 17 Cov.: 0 AF XY: 0.210 AC XY: 77AN XY: 366
GnomAD4 genome AF: 0.161 AC: 24465AN: 152234Hom.: 2607 Cov.: 33 AF XY: 0.153 AC XY: 11413AN XY: 74428
ClinVar
Submissions by phenotype
Congenital heart disease Pathogenic:1Benign:1
NM_002052.3:c.*852G>A in the gene GATA4 has an allele frequency of 0.228 in European (non-Finnish) subpopulation in the gnomAD database. 460 homozygous occurrences are observed in the gnomAD database. This evidence suggests the variant to be classified as benign. ACMG/AMP criteria applied: BA1; BS2. -
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not provided Benign:2
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GATA4-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at